Loading required package: knitr
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(as ‘lib’ is unspecified)
also installing the dependencies ‘mime’, ‘stringi’, ‘magrittr’, ‘htmltools’, ‘caTools’, ‘bitops’, ‘evaluate’, ‘digest’, ‘formatR’, ‘highr’, ‘markdown’, ‘stringr’, ‘yaml’, ‘testit’, ‘rgl’, ‘rmarkdown’, ‘XML’, ‘RCurl’

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* installing *source* package ‘mime’ ...
** package ‘mime’ successfully unpacked and MD5 sums checked
** libs
installing to /home/ubuntu/R_libs/mime/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (mime)
* installing *source* package ‘stringi’ ...
** package ‘stringi’ successfully unpacked and MD5 sums checked
** libs
In file included from icu55/unicode/platform.h:23:0,
from icu55/unicode/ptypes.h:50,
from icu55/unicode/umachine.h:44,
from icu55/unicode/utypes.h:36,
from icu55/common/uidna.cpp:17:
icu55/common/uidna.cpp: In function ‘int32_t _internal_toUnicode(const UChar*, int32_t, UChar*, int32_t, int32_t, UStringPrepProfile*, UParseError*, UErrorCode*)’:
icu55/unicode/urename.h:979:48: warning: ‘int32_t uidna_toASCII_55(const UChar*, int32_t, UChar*, int32_t, int32_t, UParseError*, UErrorCode*)’ is deprecated (declared at icu55/unicode/uidna.h:574) [-Wdeprecated-declarations]
#define uidna_toASCII U_ICU_ENTRY_POINT_RENAME(uidna_toASCII)
^
icu55/unicode/uvernum.h:110:43: note: in definition of macro ‘U_DEF_ICU_ENTRY_POINT_RENAME’
#define U_DEF_ICU_ENTRY_POINT_RENAME(x,y) x ## y
^
icu55/unicode/uvernum.h:112:40: note: in expansion of macro ‘U_DEF2_ICU_ENTRY_POINT_RENAME’
#define U_ICU_ENTRY_POINT_RENAME(x) U_DEF2_ICU_ENTRY_POINT_RENAME(x,U_ICU_VERSION_SUFFIX)
^
icu55/unicode/urename.h:979:23: note: in expansion of macro ‘U_ICU_ENTRY_POINT_RENAME’
#define uidna_toASCII U_ICU_ENTRY_POINT_RENAME(uidna_toASCII)
^
icu55/common/uidna.cpp:513:17: note: in expansion of macro ‘uidna_toASCII’
b3Len = uidna_toASCII(b2, b2Len, b3, b3Capacity, options, parseError, status);
^
icu55/common/uidna.cpp:513:85: warning: ‘int32_t uidna_toASCII_55(const UChar*, int32_t, UChar*, int32_t, int32_t, UParseError*, UErrorCode*)’ is deprecated (declared at icu55/unicode/uidna.h:574) [-Wdeprecated-declarations]
b3Len = uidna_toASCII(b2, b2Len, b3, b3Capacity, options, parseError, status);
^
In file included from icu55/unicode/platform.h:23:0,
from icu55/unicode/ptypes.h:50,
from icu55/unicode/umachine.h:44,
from icu55/unicode/utypes.h:36,
from icu55/common/uidna.cpp:17:
icu55/unicode/urename.h:979:48: warning: ‘int32_t uidna_toASCII_55(const UChar*, int32_t, UChar*, int32_t, int32_t, UParseError*, UErrorCode*)’ is deprecated (declared at icu55/unicode/uidna.h:574) [-Wdeprecated-declarations]
#define uidna_toASCII U_ICU_ENTRY_POINT_RENAME(uidna_toASCII)
^
icu55/unicode/uvernum.h:110:43: note: in definition of macro ‘U_DEF_ICU_ENTRY_POINT_RENAME’
#define U_DEF_ICU_ENTRY_POINT_RENAME(x,y) x ## y
^
icu55/unicode/uvernum.h:112:40: note: in expansion of macro ‘U_DEF2_ICU_ENTRY_POINT_RENAME’
#define U_ICU_ENTRY_POINT_RENAME(x) U_DEF2_ICU_ENTRY_POINT_RENAME(x,U_ICU_VERSION_SUFFIX)
^
icu55/unicode/urename.h:979:23: note: in expansion of macro ‘U_ICU_ENTRY_POINT_RENAME’
#define uidna_toASCII U_ICU_ENTRY_POINT_RENAME(uidna_toASCII)
^
icu55/common/uidna.cpp:526:22: note: in expansion of macro ‘uidna_toASCII’
b3Len = uidna_toASCII(b2,b2Len,b3,b3Len,options,parseError, status);
^
icu55/common/uidna.cpp:526:80: warning: ‘int32_t uidna_toASCII_55(const UChar*, int32_t, UChar*, int32_t, int32_t, UParseError*, UErrorCode*)’ is deprecated (declared at icu55/unicode/uidna.h:574) [-Wdeprecated-declarations]
b3Len = uidna_toASCII(b2,b2Len,b3,b3Len,options,parseError, status);
^
In file included from icu55/unicode/platform.h:23:0,
from icu55/unicode/ptypes.h:50,
from icu55/unicode/umachine.h:44,
from icu55/unicode/utypes.h:36,
from icu55/common/uidna.cpp:17:
icu55/common/uidna.cpp: In function ‘int32_t uidna_compare_55(const UChar*, int32_t, const UChar*, int32_t, int32_t, UErrorCode*)’:
icu55/unicode/urename.h:966:51: warning: ‘int32_t uidna_IDNToASCII_55(const UChar*, int32_t, UChar*, int32_t, int32_t, UParseError*, UErrorCode*)’ is deprecated (declared at icu55/common/uidna.cpp:668) [-Wdeprecated-declarations]
#define uidna_IDNToASCII U_ICU_ENTRY_POINT_RENAME(uidna_IDNToASCII)
^
icu55/unicode/uvernum.h:110:43: note: in definition of macro ‘U_DEF_ICU_ENTRY_POINT_RENAME’
#define U_DEF_ICU_ENTRY_POINT_RENAME(x,y) x ## y
^
icu55/unicode/uvernum.h:112:40: note: in expansion of macro ‘U_DEF2_ICU_ENTRY_POINT_RENAME’
#define U_ICU_ENTRY_POINT_RENAME(x) U_DEF2_ICU_ENTRY_POINT_RENAME(x,U_ICU_VERSION_SUFFIX)
^
icu55/unicode/urename.h:966:26: note: in expansion of macro ‘U_ICU_ENTRY_POINT_RENAME’
#define uidna_IDNToASCII U_ICU_ENTRY_POINT_RENAME(uidna_IDNToASCII)
^
icu55/common/uidna.cpp:876:13: note: in expansion of macro ‘uidna_IDNToASCII’
b1Len = uidna_IDNToASCII(s1, length1, b1, b1Capacity, options, &parseError, status);
^
icu55/common/uidna.cpp:876:87: warning: ‘int32_t uidna_IDNToASCII_55(const UChar*, int32_t, UChar*, int32_t, int32_t, UParseError*, UErrorCode*)’ is deprecated (declared at icu55/common/uidna.cpp:668) [-Wdeprecated-declarations]
b1Len = uidna_IDNToASCII(s1, length1, b1, b1Capacity, options, &parseError, status);
^
In file included from icu55/unicode/platform.h:23:0,
from icu55/unicode/ptypes.h:50,
from icu55/unicode/umachine.h:44,
from icu55/unicode/utypes.h:36,
from icu55/common/uidna.cpp:17:
icu55/unicode/urename.h:966:51: warning: ‘int32_t uidna_IDNToASCII_55(const UChar*, int32_t, UChar*, int32_t, int32_t, UParseError*, UErrorCode*)’ is deprecated (declared at icu55/common/uidna.cpp:668) [-Wdeprecated-declarations]
#define uidna_IDNToASCII U_ICU_ENTRY_POINT_RENAME(uidna_IDNToASCII)
^
icu55/unicode/uvernum.h:110:43: note: in definition of macro ‘U_DEF_ICU_ENTRY_POINT_RENAME’
#define U_DEF_ICU_ENTRY_POINT_RENAME(x,y) x ## y
^
icu55/unicode/uvernum.h:112:40: note: in expansion of macro ‘U_DEF2_ICU_ENTRY_POINT_RENAME’
#define U_ICU_ENTRY_POINT_RENAME(x) U_DEF2_ICU_ENTRY_POINT_RENAME(x,U_ICU_VERSION_SUFFIX)
^
icu55/unicode/urename.h:966:26: note: in expansion of macro ‘U_ICU_ENTRY_POINT_RENAME’
#define uidna_IDNToASCII U_ICU_ENTRY_POINT_RENAME(uidna_IDNToASCII)
^
icu55/common/uidna.cpp:887:17: note: in expansion of macro ‘uidna_IDNToASCII’
b1Len = uidna_IDNToASCII(s1,length1,b1,b1Len, options, &parseError, status);
^
icu55/common/uidna.cpp:887:83: warning: ‘int32_t uidna_IDNToASCII_55(const UChar*, int32_t, UChar*, int32_t, int32_t, UParseError*, UErrorCode*)’ is deprecated (declared at icu55/common/uidna.cpp:668) [-Wdeprecated-declarations]
b1Len = uidna_IDNToASCII(s1,length1,b1,b1Len, options, &parseError, status);
^
In file included from icu55/unicode/platform.h:23:0,
from icu55/unicode/ptypes.h:50,
from icu55/unicode/umachine.h:44,
from icu55/unicode/utypes.h:36,
from icu55/common/uidna.cpp:17:
icu55/unicode/urename.h:966:51: warning: ‘int32_t uidna_IDNToASCII_55(const UChar*, int32_t, UChar*, int32_t, int32_t, UParseError*, UErrorCode*)’ is deprecated (declared at icu55/common/uidna.cpp:668) [-Wdeprecated-declarations]
#define uidna_IDNToASCII U_ICU_ENTRY_POINT_RENAME(uidna_IDNToASCII)
^
icu55/unicode/uvernum.h:110:43: note: in definition of macro ‘U_DEF_ICU_ENTRY_POINT_RENAME’
#define U_DEF_ICU_ENTRY_POINT_RENAME(x,y) x ## y
^
icu55/unicode/uvernum.h:112:40: note: in expansion of macro ‘U_DEF2_ICU_ENTRY_POINT_RENAME’
#define U_ICU_ENTRY_POINT_RENAME(x) U_DEF2_ICU_ENTRY_POINT_RENAME(x,U_ICU_VERSION_SUFFIX)
^
icu55/unicode/urename.h:966:26: note: in expansion of macro ‘U_ICU_ENTRY_POINT_RENAME’
#define uidna_IDNToASCII U_ICU_ENTRY_POINT_RENAME(uidna_IDNToASCII)
^
icu55/common/uidna.cpp:891:13: note: in expansion of macro ‘uidna_IDNToASCII’
b2Len = uidna_IDNToASCII(s2,length2, b2,b2Capacity, options, &parseError, status);
^
icu55/common/uidna.cpp:891:85: warning: ‘int32_t uidna_IDNToASCII_55(const UChar*, int32_t, UChar*, int32_t, int32_t, UParseError*, UErrorCode*)’ is deprecated (declared at icu55/common/uidna.cpp:668) [-Wdeprecated-declarations]
b2Len = uidna_IDNToASCII(s2,length2, b2,b2Capacity, options, &parseError, status);
^
In file included from icu55/unicode/platform.h:23:0,
from icu55/unicode/ptypes.h:50,
from icu55/unicode/umachine.h:44,
from icu55/unicode/utypes.h:36,
from icu55/common/uidna.cpp:17:
icu55/unicode/urename.h:966:51: warning: ‘int32_t uidna_IDNToASCII_55(const UChar*, int32_t, UChar*, int32_t, int32_t, UParseError*, UErrorCode*)’ is deprecated (declared at icu55/common/uidna.cpp:668) [-Wdeprecated-declarations]
#define uidna_IDNToASCII U_ICU_ENTRY_POINT_RENAME(uidna_IDNToASCII)
^
icu55/unicode/uvernum.h:110:43: note: in definition of macro ‘U_DEF_ICU_ENTRY_POINT_RENAME’
#define U_DEF_ICU_ENTRY_POINT_RENAME(x,y) x ## y
^
icu55/unicode/uvernum.h:112:40: note: in expansion of macro ‘U_DEF2_ICU_ENTRY_POINT_RENAME’
#define U_ICU_ENTRY_POINT_RENAME(x) U_DEF2_ICU_ENTRY_POINT_RENAME(x,U_ICU_VERSION_SUFFIX)
^
icu55/unicode/urename.h:966:26: note: in expansion of macro ‘U_ICU_ENTRY_POINT_RENAME’
#define uidna_IDNToASCII U_ICU_ENTRY_POINT_RENAME(uidna_IDNToASCII)
^
icu55/common/uidna.cpp:902:17: note: in expansion of macro ‘uidna_IDNToASCII’
b2Len = uidna_IDNToASCII(s2, length2, b2, b2Len, options, &parseError, status);
^
icu55/common/uidna.cpp:902:86: warning: ‘int32_t uidna_IDNToASCII_55(const UChar*, int32_t, UChar*, int32_t, int32_t, UParseError*, UErrorCode*)’ is deprecated (declared at icu55/common/uidna.cpp:668) [-Wdeprecated-declarations]
b2Len = uidna_IDNToASCII(s2, length2, b2, b2Len, options, &parseError, status);
^
In file included from icu55/unicode/platform.h:23:0,
from icu55/unicode/ptypes.h:50,
from icu55/unicode/umachine.h:44,
from icu55/unicode/utypes.h:36,
from icu55/unicode/ustring.h:19,
from icu55/i18n/ucol_sit.cpp:16:
icu55/i18n/ucol_sit.cpp: In function ‘UCollator* ucol_openFromShortString_55(const char*, UBool, UParseError*, UErrorCode*)’:
icu55/unicode/urename.h:758:54: warning: ‘uint32_t ucol_setVariableTop_55(UCollator*, const UChar*, int32_t, UErrorCode*)’ is deprecated (declared at icu55/unicode/ucol.h:1254) [-Wdeprecated-declarations]
#define ucol_setVariableTop U_ICU_ENTRY_POINT_RENAME(ucol_setVariableTop)
^
icu55/unicode/uvernum.h:110:43: note: in definition of macro ‘U_DEF_ICU_ENTRY_POINT_RENAME’
#define U_DEF_ICU_ENTRY_POINT_RENAME(x,y) x ## y
^
icu55/unicode/uvernum.h:112:40: note: in expansion of macro ‘U_DEF2_ICU_ENTRY_POINT_RENAME’
#define U_ICU_ENTRY_POINT_RENAME(x) U_DEF2_ICU_ENTRY_POINT_RENAME(x,U_ICU_VERSION_SUFFIX)
^
icu55/unicode/urename.h:758:29: note: in expansion of macro ‘U_ICU_ENTRY_POINT_RENAME’
#define ucol_setVariableTop U_ICU_ENTRY_POINT_RENAME(ucol_setVariableTop)
^
icu55/i18n/ucol_sit.cpp:543:13: note: in expansion of macro ‘ucol_setVariableTop’
ucol_setVariableTop(result, s.variableTopString, s.variableTopStringLen, status);
^
icu55/i18n/ucol_sit.cpp:543:92: warning: ‘uint32_t ucol_setVariableTop_55(UCollator*, const UChar*, int32_t, UErrorCode*)’ is deprecated (declared at icu55/unicode/ucol.h:1254) [-Wdeprecated-declarations]
ucol_setVariableTop(result, s.variableTopString, s.variableTopStringLen, status);
^
In file included from icu55/unicode/platform.h:23:0,
from icu55/unicode/ptypes.h:50,
from icu55/unicode/umachine.h:44,
from icu55/unicode/utypes.h:36,
from icu55/unicode/ustring.h:19,
from icu55/i18n/ucol_sit.cpp:16:
icu55/unicode/urename.h:749:58: warning: ‘void ucol_restoreVariableTop_55(UCollator*, uint32_t, UErrorCode*)’ is deprecated (declared at icu55/unicode/ucol.h:1286) [-Wdeprecated-declarations]
#define ucol_restoreVariableTop U_ICU_ENTRY_POINT_RENAME(ucol_restoreVariableTop)
^
icu55/unicode/uvernum.h:110:43: note: in definition of macro ‘U_DEF_ICU_ENTRY_POINT_RENAME’
#define U_DEF_ICU_ENTRY_POINT_RENAME(x,y) x ## y
^
icu55/unicode/uvernum.h:112:40: note: in expansion of macro ‘U_DEF2_ICU_ENTRY_POINT_RENAME’
#define U_ICU_ENTRY_POINT_RENAME(x) U_DEF2_ICU_ENTRY_POINT_RENAME(x,U_ICU_VERSION_SUFFIX)
^
icu55/unicode/urename.h:749:33: note: in expansion of macro ‘U_ICU_ENTRY_POINT_RENAME’
#define ucol_restoreVariableTop U_ICU_ENTRY_POINT_RENAME(ucol_restoreVariableTop)
^
icu55/i18n/ucol_sit.cpp:545:13: note: in expansion of macro ‘ucol_restoreVariableTop’
ucol_restoreVariableTop(result, s.variableTopValue, status);
^
icu55/i18n/ucol_sit.cpp:545:71: warning: ‘void ucol_restoreVariableTop_55(UCollator*, uint32_t, UErrorCode*)’ is deprecated (declared at icu55/unicode/ucol.h:1286) [-Wdeprecated-declarations]
ucol_restoreVariableTop(result, s.variableTopValue, status);
^
installing via 'install.libs.R' to /home/ubuntu/R_libs/stringi
downloading ICU data library (icudt)
the files will be extracted to: /home/ubuntu/R_libs/stringi/libs
no icudt in a local repo
trying URL 'http://static.rexamine.com/packages/icudt55l.zip'
Content type 'application/zip' length 10176327 bytes (9.7 MB)
==================================================
downloaded 9.7 MB

icudt fetch OK
decompressing downloaded archive
icudt has been installed successfully
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (stringi)
* installing *source* package ‘magrittr’ ...
** package ‘magrittr’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (magrittr)
* installing *source* package ‘bitops’ ...
** package ‘bitops’ successfully unpacked and MD5 sums checked
** libs
installing to /home/ubuntu/R_libs/bitops/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (bitops)
* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** libs
installing to /home/ubuntu/R_libs/digest/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (digest)
* installing *source* package ‘formatR’ ...
** package ‘formatR’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (formatR)
* installing *source* package ‘highr’ ...
** package ‘highr’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (highr)
* installing *source* package ‘yaml’ ...
** package ‘yaml’ successfully unpacked and MD5 sums checked
** libs
installing to /home/ubuntu/R_libs/yaml/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (yaml)
* installing *source* package ‘testit’ ...
** package ‘testit’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (testit)
* installing *source* package ‘rgl’ ...
** package ‘rgl’ successfully unpacked and MD5 sums checked
configure: error: X11 not found but required, configure aborted.
ERROR: configuration failed for package ‘rgl’
* removing ‘/home/ubuntu/R_libs/rgl’
* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
** libs
NodeGC.c: In function ‘clearNodeMemoryManagement’:
NodeGC.c:385:96: warning: comparison between pointer and integer [enabled by default]
int isOurs = (a = node->_private != &R_XML_NoMemoryMgmt) && (b = ((int *)(node->_private))[1] == (int *) &R_XML_MemoryMgrMarker);
^
XMLTree.c: In function ‘R_xmlSearchNs’:
XMLTree.c:1695:39: warning: comparison of distinct pointer types lacks a cast [enabled by default]
xmlDocPtr doc = (xmlDocPtr) r_doc == NULL_USER_OBJECT ? NULL : R_ExternalPtrAddr(r_doc);
^
installing to /home/ubuntu/R_libs/XML/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘source’ from package ‘base’ in package ‘XML’
in method for ‘xmlAttrsToDataFrame’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘readKeyValueDB’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘readSolrDoc’ with signature ‘"AsIs"’: no definition for class “AsIs”
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (XML)
* installing *source* package ‘htmltools’ ...
** package ‘htmltools’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (htmltools)
* installing *source* package ‘caTools’ ...
** package ‘caTools’ successfully unpacked and MD5 sums checked
** libs
installing to /home/ubuntu/R_libs/caTools/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (caTools)
* installing *source* package ‘markdown’ ...
** package ‘markdown’ successfully unpacked and MD5 sums checked
** libs
installing to /home/ubuntu/R_libs/markdown/libs
** R
** inst
** preparing package for lazy loading
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Loading required package: knitr
Warning messages:
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there is no package called ‘knitr’
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Loading required package: WGCNA
Installing package into ‘/home/ubuntu/R_libs’
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* installing *source* package ‘colorspace’ ...
** package ‘colorspace’ successfully unpacked and MD5 sums checked
** libs
installing to /home/ubuntu/R_libs/colorspace/libs
** R
** data
*** moving datasets to lazyload DB
** inst
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Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘colorspace’
** help
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** building package indices
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* DONE (colorspace)
* installing *source* package ‘RColorBrewer’ ...
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* installing *source* package ‘dichromat’ ...
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** data
** preparing package for lazy loading
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* DONE (dichromat)
* installing *source* package ‘labeling’ ...
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* installing *source* package ‘Rcpp’ ...
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* DONE (proto)
* installing *source* package ‘acepack’ ...
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* DONE (iterators)
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* installing *source* package ‘fastcluster’ ...
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* installing *source* package ‘matrixStats’ ...
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installing to /home/ubuntu/R_libs/infotheo/libs
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* installing *source* package ‘plyr’ ...
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* DONE (plyr)
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* installing *source* package ‘reshape2’ ...
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ERROR: dependencies ‘impute’, ‘preprocessCore’, ‘GO.db’, ‘AnnotationDbi’ are not available for package ‘WGCNA’
* removing ‘/home/ubuntu/R_libs/WGCNA’
Loading required package: WGCNA
Installing package into ‘/home/ubuntu/R_libs’
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Bioconductor version 3.1 (BiocInstaller 1.18.3), ?biocLite for help
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.3), R version 3.2.1.
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* installing *source* package ‘BiocGenerics’ ...
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** help
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* installing *source* package ‘DBI’ ...
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* installing *source* package ‘impute’ ...
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* installing *source* package ‘preprocessCore’ ...
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* installing *source* package ‘Biobase’ ...
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* installing *source* package ‘S4Vectors’ ...
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Creating a generic function for ‘by’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘window’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘head’ from package ‘utils’ in package ‘S4Vectors’
Creating a generic function for ‘tail’ from package ‘utils’ in package ‘S4Vectors’
Creating a generic function for ‘with’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘%in%’ from package ‘base’ in package ‘S4Vectors’
Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’
Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘as.table’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘t’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘rev’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘which’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘which.max’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘ifelse’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘diff’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘mean’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘var’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘sd’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘median’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘mad’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘IQR’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘levels’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘droplevels’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘within’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘aggregate’ from package ‘stats’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (S4Vectors)
* installing *source* package ‘IRanges’ ...
** libs
common.c: In function ‘firstWordInFile’:
common.c:1787:6: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(wordBuf, wordBufSize, f);
^
installing to /home/ubuntu/R_libs/IRanges/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘window<-’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘rev’ from package ‘base’ in package ‘IRanges’
in method for ‘coerce’ with signature ‘"Hits","PartitioningByEnd"’: no definition for class “PartitioningByEnd”
in method for ‘coerce’ with signature ‘"Hits","Partitioning"’: no definition for class “Partitioning”
in method for ‘coerce’ with signature ‘"Hits","Ranges"’: no definition for class “Ranges”
in method for ‘coerce’ with signature ‘"Hits","IRanges"’: no definition for class “IRanges”
in method for ‘coerce’ with signature ‘"Hits","CompressedIntegerList"’: no definition for class “CompressedIntegerList”
in method for ‘coerce’ with signature ‘"Hits","IntegerList"’: no definition for class “IntegerList”
Creating a generic function for ‘stack’ from package ‘utils’ in package ‘IRanges’
in method for ‘!’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘match’ with signature ‘"CompressedList","list"’: no definition for class “CompressedList”
in method for ‘match’ with signature ‘"CompressedList","vector"’: no definition for class “CompressedList”
in method for ‘duplicated’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘unique’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘is.na’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
Creating a generic function for ‘mean’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which.max’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which.min’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘split’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘split<-’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘diff’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘var’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘sd’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘median’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘quantile’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘mad’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘IQR’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IRanges)
* installing *source* package ‘GenomeInfoDb’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomeInfoDb)
* installing *source* package ‘AnnotationDbi’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a generic function for ‘toString’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AnnotationDbi)
* installing *source* package ‘GO.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (GO.db)
* installing *source* package ‘WGCNA’ ...
** package ‘WGCNA’ successfully unpacked and MD5 sums checked
** libs
installing to /home/ubuntu/R_libs/WGCNA/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (WGCNA)
Old packages: 'foreign', 'Matrix', 'spatial'
Loading required package: WGCNA
Loading required package: dynamicTreeCut
Loading required package: fastcluster

Attaching package: ‘fastcluster’

The following object is masked from ‘package:stats’:

hclust

Loading required package: DBI


Attaching package: ‘WGCNA’

The following object is masked from ‘package:stats’:

cor

Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘WGCNA’
2: In install.packages(x, dep = TRUE, repos = "http://cran.rstudio.com") :
installation of package ‘WGCNA’ had non-zero exit status
3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘WGCNA’
Loading required package: DESeq
Installing package into ‘/home/ubuntu/R_libs’
(as ‘lib’ is unspecified)
Loading required package: DESeq
Bioconductor version 3.1 (BiocInstaller 1.18.3), ?biocLite for help
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.3), R version 3.2.1.
Installing package(s) ‘DESeq’
also installing the dependencies ‘xtable’, ‘annotate’, ‘locfit’, ‘genefilter’, ‘geneplotter’

trying URL 'http://cran.fhcrc.org/src/contrib/xtable_1.7-4.tar.gz'
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trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/annotate_1.46.0.tar.gz'
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trying URL 'http://cran.fhcrc.org/src/contrib/locfit_1.5-9.1.tar.gz'
Content type 'application/x-gzip' length 196560 bytes (191 KB)
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trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/genefilter_1.50.0.tar.gz'
Content type 'application/x-gzip' length 1291651 bytes (1.2 MB)
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trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/geneplotter_1.46.0.tar.gz'
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trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/DESeq_1.20.0.tar.gz'
Content type 'application/x-gzip' length 1731608 bytes (1.7 MB)
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* installing *source* package ‘xtable’ ...
** package ‘xtable’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (xtable)
* installing *source* package ‘locfit’ ...
** package ‘locfit’ successfully unpacked and MD5 sums checked
** libs
installing to /home/ubuntu/R_libs/locfit/libs
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (locfit)
* installing *source* package ‘annotate’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (annotate)
* installing *source* package ‘genefilter’ ...
** libs
installing to /home/ubuntu/R_libs/genefilter/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘genefilter’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genefilter)
* installing *source* package ‘geneplotter’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (geneplotter)
* installing *source* package ‘DESeq’ ...
** libs
installing to /home/ubuntu/R_libs/DESeq/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DESeq)
Old packages: 'foreign', 'Matrix', 'spatial'
Loading required package: DESeq
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unlist, unsplit

Loading required package: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: lattice
Welcome to 'DESeq'. For improved performance, usability and
functionality, please consider migrating to 'DESeq2'.
Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘DESeq’
2: package ‘DESeq’ is not available (for R version 3.2.1)
3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘DESeq’
Loading required package: RColorBrewer
Loading required package: vsn
Installing package into ‘/home/ubuntu/R_libs’
(as ‘lib’ is unspecified)
Loading required package: vsn
Bioconductor version 3.1 (BiocInstaller 1.18.3), ?biocLite for help
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.3), R version 3.2.1.
Installing package(s) ‘vsn’
also installing the dependencies ‘affyio’, ‘zlibbioc’, ‘affy’, ‘limma’

trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/affyio_1.36.0.tar.gz'
Content type 'application/x-gzip' length 105804 bytes (103 KB)
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trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/zlibbioc_1.14.0.tar.gz'
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trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/affy_1.46.1.tar.gz'
Content type 'application/x-gzip' length 1315042 bytes (1.3 MB)
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trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/limma_3.24.12.tar.gz'
Content type 'application/x-gzip' length 1436837 bytes (1.4 MB)
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trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/vsn_3.36.0.tar.gz'
Content type 'application/x-gzip' length 1423571 bytes (1.4 MB)
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* installing *source* package ‘zlibbioc’ ...
** libs
installing to /home/ubuntu/R_libs/zlibbioc/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (zlibbioc)
* installing *source* package ‘limma’ ...
** libs
installing to /home/ubuntu/R_libs/limma/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (limma)
* installing *source* package ‘affyio’ ...
** libs
fread_functions.c: In function ‘gzread_int32’:
fread_functions.c:414:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(int)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_uint32’:
fread_functions.c:439:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(unsigned int)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_int16’:
fread_functions.c:458:4: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(short)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_uint16’:
fread_functions.c:476:4: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(unsigned short)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_float32’:
fread_functions.c:497:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(float)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_char’:
fread_functions.c:513:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(char)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_uchar’:
fread_functions.c:529:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(unsigned char)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_double64’:
fread_functions.c:547:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream, destination,sizeof(double)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_be_int32’:
fread_functions.c:575:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(int)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_be_uint32’:
fread_functions.c:600:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(unsigned int)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_be_int16’:
fread_functions.c:620:4: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(short)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_be_uint16’:
fread_functions.c:636:4: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(unsigned short)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_be_float32’:
fread_functions.c:656:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(float)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_be_char’:
fread_functions.c:673:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(char)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_be_uchar’:
fread_functions.c:690:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream,destination,sizeof(unsigned char)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
fread_functions.c: In function ‘gzread_be_double64’:
fread_functions.c:706:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
result = gzread(instream, destination,sizeof(double)*n);
^
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
read_abatch.c: In function ‘gz_get_detailed_header_info’:
read_abatch.c:1989:15: warning: assignment from incompatible pointer type [enabled by default]
currentFile = open_gz_cel_file(filename);
^
read_abatch.c:1991:3: warning: passing argument 1 of ‘gzAdvanceToSection’ from incompatible pointer type [enabled by default]
gzAdvanceToSection(currentFile,"[HEADER]",buffer);
^
read_abatch.c:1439:13: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){
^
read_abatch.c:1993:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"Cols",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:1998:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"Rows",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2003:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"GridCornerUL",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2009:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"GridCornerUR",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2015:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"GridCornerLR",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2021:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"GridCornerLL",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2027:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"DatHeader",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2059:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"Algorithm",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2067:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"AlgorithmParameters",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2072:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(currentFile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘gz_get_masks_outliers’:
read_abatch.c:2100:15: warning: assignment from incompatible pointer type [enabled by default]
currentFile = open_gz_cel_file(filename);
^
read_abatch.c:2104:3: warning: passing argument 1 of ‘gzAdvanceToSection’ from incompatible pointer type [enabled by default]
gzAdvanceToSection(currentFile,"[MASKS]",buffer);
^
read_abatch.c:1439:13: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){
^
read_abatch.c:2105:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"NumberCells=",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2109:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"CellHeader=",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2118:5: warning: passing argument 3 of ‘ReadgzFileLine’ from incompatible pointer type [enabled by default]
ReadgzFileLine(buffer, BUF_SIZE, currentFile);
^
read_abatch.c:1354:13: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void ReadgzFileLine(char *buffer, int buffersize, gzFile currentFile){
^
read_abatch.c:2133:3: warning: passing argument 1 of ‘gzAdvanceToSection’ from incompatible pointer type [enabled by default]
gzAdvanceToSection(currentFile,"[OUTLIERS]",buffer);
^
read_abatch.c:1439:13: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){
^
read_abatch.c:2134:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"NumberCells=",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2138:3: warning: passing argument 1 of ‘gzfindStartsWith’ from incompatible pointer type [enabled by default]
gzfindStartsWith(currentFile,"CellHeader=",buffer);
^
read_abatch.c:1416:14: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2146:5: warning: passing argument 3 of ‘ReadgzFileLine’ from incompatible pointer type [enabled by default]
ReadgzFileLine(buffer, BUF_SIZE, currentFile);
^
read_abatch.c:1354:13: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
static void ReadgzFileLine(char *buffer, int buffersize, gzFile currentFile){
^
read_abatch.c:2158:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(currentFile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘isgzBinaryCelFile’:
read_abatch.c:3141:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_abatch.c:3148:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3153:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3159:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3164:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3169:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘gzread_binary_header’:
read_abatch.c:3192:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_abatch.c:3247:3: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [enabled by default]
if (!gzread(infile,this_header->header,sizeof(char)*this_header->header_len)){
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
read_abatch.c:3289:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘gzread_binarycel_file_intensities’:
read_abatch.c:3591:2: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->gzinfile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3597:2: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->infile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct FILE *’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3607:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->gzinfile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘gzread_binarycel_file_stddev’:
read_abatch.c:3644:2: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->gzinfile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3654:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->gzinfile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘gzread_binarycel_file_npixels’:
read_abatch.c:3692:2: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->infile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct FILE *’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3702:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->gzinfile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘gz_binary_apply_masks’:
read_abatch.c:3735:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(my_header->infile,my_header->n_cells*sizeofrecords,SEEK_CUR);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct FILE *’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_abatch.c:3748:5: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(my_header->gzinfile,my_header->n_masks*sizeof(cur_loc),SEEK_CUR);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_abatch.c:3761:5: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(my_header->gzinfile,my_header->n_outliers*sizeof(cur_loc),SEEK_CUR);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_abatch.c:3764:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->gzinfile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c: In function ‘gzbinary_get_masks_outliers’:
read_abatch.c:3797:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(my_header->gzinfile,my_header->n_cells*sizeofrecords,SEEK_CUR);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_abatch.c:3827:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(my_header->gzinfile);
^
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c: In function ‘isgzGenericCelFile’:
read_celfile_generic.c:1067:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1074:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c:1080:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c:1089:4: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c:1094:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c: In function ‘gzgeneric_get_header_info’:
read_celfile_generic.c:1115:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1151:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c: In function ‘gzgeneric_get_detailed_header_info’:
read_celfile_generic.c:1175:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1633:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c: In function ‘check_gzgeneric_cel_file’:
read_celfile_generic.c:1661:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1701:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c: In function ‘gzread_genericcel_file_intensities’:
read_celfile_generic.c:1726:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1745:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c: In function ‘gzread_genericcel_file_stddev’:
read_celfile_generic.c:1777:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1790:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1802:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c: In function ‘gzread_genericcel_file_npixels’:
read_celfile_generic.c:1831:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1844:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1848:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1861:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c: In function ‘gzgeneric_get_masks_outliers’:
read_celfile_generic.c:1896:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1910:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1915:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1920:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1939:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1960:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c: In function ‘gzgeneric_apply_masks’:
read_celfile_generic.c:1991:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:2012:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:2017:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:2022:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:2038:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:2056:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_generic.c: In function ‘gzread_ASTRING_fw’:
read_generic.c:927:2: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(instream, length-destination->len, SEEK_CUR);
^
In file included from fread_functions.h:12:0,
from read_generic.c:50:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_generic.c: In function ‘gzread_AWSTRING_fw’:
read_generic.c:973:2: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(instream, length-2*destination->len, SEEK_CUR);
^
In file included from fread_functions.h:12:0,
from read_generic.c:50:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_generic.c: In function ‘gzRead_Generic’:
read_generic.c:1508:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(cur_file_name, "rb")) == NULL)
^
read_generic.c:1540:7: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from fread_functions.h:12:0,
from read_generic.c:50:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c: In function ‘isgzGenericMultiChannelCelFile’:
read_multichannel_celfile_generic.c:620:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:627:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c:633:5: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c:642:4: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c:647:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c: In function ‘gzmultichannel_determine_number_channels’:
read_multichannel_celfile_generic.c:677:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:701:5: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile,next_group,SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:704:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c: In function ‘gzmultichannel_determine_channel_name’:
read_multichannel_celfile_generic.c:729:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:741:5: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile,next_group,SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:751:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c: In function ‘gzread_genericcel_file_intensities_multichannel’:
read_multichannel_celfile_generic.c:778:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:793:5: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile,next_group,SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:807:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c: In function ‘gzread_genericcel_file_stddev_multichannel’:
read_multichannel_celfile_generic.c:834:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:849:5: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile,next_group,SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:856:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:867:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c: In function ‘gzread_genericcel_file_npixels_multichannel’:
read_multichannel_celfile_generic.c:896:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:912:5: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile,next_group,SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:919:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:923:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:936:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c: In function ‘gzgeneric_get_masks_outliers_multichannel’:
read_multichannel_celfile_generic.c:965:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:981:5: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile,next_group,SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:989:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:994:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:999:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:1018:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:1039:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c: In function ‘gzgeneric_apply_masks_multichannel’:
read_multichannel_celfile_generic.c:1069:15: warning: assignment from incompatible pointer type [enabled by default]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:1090:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:1095:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:1100:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:1116:3: warning: passing argument 1 of ‘gzseek’ from incompatible pointer type [enabled by default]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_multichannel_celfile_generic.c:1134:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_pgf.c: In function ‘pgf_count_probeset_types’:
read_pgf.c:1265:28: warning: assignment from incompatible pointer type [enabled by default]
my_pgf->probesets->current= my_pgf->probesets->current->next;
^
installing to /home/ubuntu/R_libs/affyio/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (affyio)
* installing *source* package ‘affy’ ...
** libs
installing to /home/ubuntu/R_libs/affy/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘open’ from package ‘base’ in package ‘affy’
Creating a generic function for ‘close’ from package ‘base’ in package ‘affy’
Creating a generic function for ‘barplot’ from package ‘graphics’ in package ‘affy’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (affy)
* installing *source* package ‘vsn’ ...
** libs
installing to /home/ubuntu/R_libs/vsn/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘logLik’ from package ‘stats’ in package ‘vsn’
Creating a generic function for ‘coef’ from package ‘stats’ in package ‘vsn’
Creating a generic function for ‘coefficients’ from package ‘stats’ in package ‘vsn’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (vsn)
Old packages: 'foreign', 'Matrix', 'spatial'
Loading required package: vsn
Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘vsn’
2: package ‘vsn’ is not available (for R version 3.2.1)
3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘vsn’
Loading required package: gplots
Installing package into ‘/home/ubuntu/R_libs’
(as ‘lib’ is unspecified)
also installing the dependencies ‘gtools’, ‘gdata’

trying URL 'http://cran.rstudio.com/src/contrib/gtools_3.5.0.tar.gz'
Content type 'application/x-gzip' length 64855 bytes (63 KB)
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trying URL 'http://cran.rstudio.com/src/contrib/gdata_2.17.0.tar.gz'
Content type 'application/x-gzip' length 1041264 bytes (1016 KB)
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trying URL 'http://cran.rstudio.com/src/contrib/gplots_2.17.0.tar.gz'
Content type 'application/x-gzip' length 629789 bytes (615 KB)
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* installing *source* package ‘gtools’ ...
** package ‘gtools’ successfully unpacked and MD5 sums checked
** libs
installing to /home/ubuntu/R_libs/gtools/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (gtools)
* installing *source* package ‘gdata’ ...
** package ‘gdata’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gdata)
* installing *source* package ‘gplots’ ...
** package ‘gplots’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gplots)
Loading required package: gplots

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

lowess

Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘gplots’
Loading required package: knitr
Loading required package: markdown


processing file: /home/ubuntu/myconnectome/myconnectome/qa/QA_summary_rsfmri.Rmd
output file: /home/ubuntu/myconnectome/rsfmri/QA_summary_rsfmri.md

Loading required package: knitr
Loading required package: markdown


processing file: /home/ubuntu/myconnectome/myconnectome/rnaseq/RNAseq_data_preparation.Rmd
Loading required package: BiocGenerics
Loading required package: methods
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from 'package:stats':

xtabs

The following objects are masked from 'package:base':

anyDuplicated, append, as.data.frame, as.vector, cbind,
colnames, do.call, duplicated, eval, evalq, Filter, Find, get,
intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rep.int, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unlist, unsplit

Loading required package: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: lattice
Welcome to 'DESeq'. For improved performance, usability and
functionality, please consider migrating to 'DESeq2'.

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Welcome to 'DESeq'. For improved performance, usability and
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output file: /home/ubuntu/myconnectome/rna-seq/snyderome/Snyderome_data_preparation.md

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* installing *source* package ‘kernlab’ ...
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* installing *source* package ‘memoise’ ...
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processing file: /home/ubuntu/myconnectome/myconnectome/timeseries/timeseries_analyses.Rmd
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processing file: /home/ubuntu/myconnectome/myconnectome/timeseries/Make_timeseries_plots.Rmd
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processing file: /home/ubuntu/myconnectome/myconnectome/timeseries/Make_combined_timeseries_table.Rmd
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processing sub037 /home/ubuntu/myconnectome/combined_data_scrubbed/sub037.txt
processing sub038 /home/ubuntu/myconnectome/combined_data_scrubbed/sub038.txt
processing sub039 /home/ubuntu/myconnectome/combined_data_scrubbed/sub039.txt
processing sub040 /home/ubuntu/myconnectome/combined_data_scrubbed/sub040.txt
processing sub041 /home/ubuntu/myconnectome/combined_data_scrubbed/sub041.txt
processing sub042 /home/ubuntu/myconnectome/combined_data_scrubbed/sub042.txt
processing sub043 /home/ubuntu/myconnectome/combined_data_scrubbed/sub043.txt
processing sub044 /home/ubuntu/myconnectome/combined_data_scrubbed/sub044.txt
processing sub045 /home/ubuntu/myconnectome/combined_data_scrubbed/sub045.txt
processing sub046 /home/ubuntu/myconnectome/combined_data_scrubbed/sub046.txt
processing sub047 /home/ubuntu/myconnectome/combined_data_scrubbed/sub047.txt
processing sub048 /home/ubuntu/myconnectome/combined_data_scrubbed/sub048.txt
processing sub049 /home/ubuntu/myconnectome/combined_data_scrubbed/sub049.txt
processing sub050 /home/ubuntu/myconnectome/combined_data_scrubbed/sub050.txt
processing sub051 /home/ubuntu/myconnectome/combined_data_scrubbed/sub051.txt
processing sub053 /home/ubuntu/myconnectome/combined_data_scrubbed/sub053.txt
processing sub054 /home/ubuntu/myconnectome/combined_data_scrubbed/sub054.txt
processing sub056 /home/ubuntu/myconnectome/combined_data_scrubbed/sub056.txt
processing sub057 /home/ubuntu/myconnectome/combined_data_scrubbed/sub057.txt
processing sub058 /home/ubuntu/myconnectome/combined_data_scrubbed/sub058.txt
processing sub059 /home/ubuntu/myconnectome/combined_data_scrubbed/sub059.txt
processing sub060 /home/ubuntu/myconnectome/combined_data_scrubbed/sub060.txt
processing sub061 /home/ubuntu/myconnectome/combined_data_scrubbed/sub061.txt
processing sub062 /home/ubuntu/myconnectome/combined_data_scrubbed/sub062.txt
processing sub063 /home/ubuntu/myconnectome/combined_data_scrubbed/sub063.txt
processing sub064 /home/ubuntu/myconnectome/combined_data_scrubbed/sub064.txt
processing sub065 /home/ubuntu/myconnectome/combined_data_scrubbed/sub065.txt
processing sub066 /home/ubuntu/myconnectome/combined_data_scrubbed/sub066.txt
processing sub067 /home/ubuntu/myconnectome/combined_data_scrubbed/sub067.txt
processing sub068 /home/ubuntu/myconnectome/combined_data_scrubbed/sub068.txt
processing sub069 /home/ubuntu/myconnectome/combined_data_scrubbed/sub069.txt
processing sub070 /home/ubuntu/myconnectome/combined_data_scrubbed/sub070.txt
processing sub071 /home/ubuntu/myconnectome/combined_data_scrubbed/sub071.txt
processing sub072 /home/ubuntu/myconnectome/combined_data_scrubbed/sub072.txt
processing sub073 /home/ubuntu/myconnectome/combined_data_scrubbed/sub073.txt
processing sub074 /home/ubuntu/myconnectome/combined_data_scrubbed/sub074.txt
processing sub075 /home/ubuntu/myconnectome/combined_data_scrubbed/sub075.txt
processing sub076 /home/ubuntu/myconnectome/combined_data_scrubbed/sub076.txt
processing sub077 /home/ubuntu/myconnectome/combined_data_scrubbed/sub077.txt
processing sub078 /home/ubuntu/myconnectome/combined_data_scrubbed/sub078.txt
processing sub079 /home/ubuntu/myconnectome/combined_data_scrubbed/sub079.txt
processing sub080 /home/ubuntu/myconnectome/combined_data_scrubbed/sub080.txt
processing sub081 /home/ubuntu/myconnectome/combined_data_scrubbed/sub081.txt
processing sub082 /home/ubuntu/myconnectome/combined_data_scrubbed/sub082.txt
processing sub083 /home/ubuntu/myconnectome/combined_data_scrubbed/sub083.txt
processing sub084 /home/ubuntu/myconnectome/combined_data_scrubbed/sub084.txt
processing sub085 /home/ubuntu/myconnectome/combined_data_scrubbed/sub085.txt
processing sub086 /home/ubuntu/myconnectome/combined_data_scrubbed/sub086.txt
processing sub087 /home/ubuntu/myconnectome/combined_data_scrubbed/sub087.txt
processing sub088 /home/ubuntu/myconnectome/combined_data_scrubbed/sub088.txt
processing sub089 /home/ubuntu/myconnectome/combined_data_scrubbed/sub089.txt
processing sub091 /home/ubuntu/myconnectome/combined_data_scrubbed/sub091.txt
processing sub092 /home/ubuntu/myconnectome/combined_data_scrubbed/sub092.txt
processing sub094 /home/ubuntu/myconnectome/combined_data_scrubbed/sub094.txt
processing sub095 /home/ubuntu/myconnectome/combined_data_scrubbed/sub095.txt
processing sub096 /home/ubuntu/myconnectome/combined_data_scrubbed/sub096.txt
processing sub097 /home/ubuntu/myconnectome/combined_data_scrubbed/sub097.txt
processing sub098 /home/ubuntu/myconnectome/combined_data_scrubbed/sub098.txt
processing sub099 /home/ubuntu/myconnectome/combined_data_scrubbed/sub099.txt
processing sub100 /home/ubuntu/myconnectome/combined_data_scrubbed/sub100.txt
processing sub101 /home/ubuntu/myconnectome/combined_data_scrubbed/sub101.txt
processing sub102 /home/ubuntu/myconnectome/combined_data_scrubbed/sub102.txt
processing sub103 /home/ubuntu/myconnectome/combined_data_scrubbed/sub103.txt
processing sub104 /home/ubuntu/myconnectome/combined_data_scrubbed/sub104.txt
MATLAB not available, downloading BCT results from repository
downloading rsfmri/PIpos_weighted_louvain_bct.txt
downloading rsfmri/geff_pos.txt
downloading rsfmri/modularity_weighted_louvain_bct.txt
generating network file for mon
generating network file for tues
generating network file for thurs
generating network file for all
dice(HARDI,skyra)= 0.510350487736
mean connection distances (0.0025 density)
fullcorr: 43.3700750415
l1 pcorr: 21.5050499776
l2 pcorr: 17.5961078299
task corr: 41.8760367145
dti: 13.8133095978
you need to set the DAVID_EMAIL environment variable to an email
address with access to the DAVID API (david.abcc.ncifcrf.gov/)

Running WGCNA - this could take a little while...
AMHR2 missing from data
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TRAV12-3 missing from data
TRAV13-1 missing from data
TRAV13-2 missing from data
TRAV14DV4 missing from data
TRAV16 missing from data
TRAV17 missing from data
TRAV18 missing from data
TRAV19 missing from data
TRAV20 missing from data
TRAV21 missing from data
TRAV22 missing from data
TRAV23DV6 missing from data
TRAV24 missing from data
TRAV25 missing from data
TRAV26-1 missing from data
TRAV26-2 missing from data
TRAV27 missing from data
TRAV29DV5 missing from data
TRAV30 missing from data
TRAV34 missing from data
TRAV35 missing from data
TRAV36DV7 missing from data
TRAV38-1 missing from data
TRAV38-2DV8 missing from data
TRAV39 missing from data
TRAV40 missing from data
TRAV41 missing from data
TRBC1 missing from data
TRBC2 missing from data
TRBD1 missing from data
TRBD2 missing from data
TRBJ1-1 missing from data
TRBJ1-2 missing from data
TRBJ1-3 missing from data
TRBJ1-4 missing from data
TRBJ1-5 missing from data
TRBJ1-6 missing from data
TRBJ2-1 missing from data
TRBJ2-2 missing from data
TRBJ2-3 missing from data
TRBJ2-4 missing from data
TRBJ2-5 missing from data
TRBJ2-6 missing from data
TRBJ2-7 missing from data
TRBV2 missing from data
TRBV3-1 missing from data
TRBV4-1 missing from data
TRBV4-2 missing from data
TRBV4-3 missing from data
TRBV5-1 missing from data
TRBV5-4 missing from data
TRBV5-5 missing from data
TRBV5-6 missing from data
TRBV5-7 missing from data
TRBV5-8 missing from data
TRBV6-1 missing from data
TRBV6-2 missing from data
TRBV6-3 missing from data
TRBV6-4 missing from data
TRBV6-5 missing from data
TRBV6-6 missing from data
TRBV6-7 missing from data
TRBV6-8 missing from data
TRBV6-9 missing from data
TRBV7-2 missing from data
TRBV7-3 missing from data
TRBV7-4 missing from data
TRBV7-6 missing from data
TRBV7-7 missing from data
TRBV7-8 missing from data
TRBV7-9 missing from data
TRBV9 missing from data
TRBV10-1 missing from data
TRBV10-2 missing from data
TRBV10-3 missing from data
TRBV11-1 missing from data
TRBV11-2 missing from data
TRBV11-3 missing from data
TRBV12-3 missing from data
TRBV12-4 missing from data
TRBV12-5 missing from data
TRBV13 missing from data
TRBV14 missing from data
TRBV15 missing from data
TRBV16 missing from data
TRBV17 missing from data
TRBV18 missing from data
TRBV19 missing from data
TRBV20-1 missing from data
TRBV24-1 missing from data
TRBV25-1 missing from data
TRBV27 missing from data
TRBV28 missing from data
TRBV29-1 missing from data
TRBV30 missing from data
TRDC missing from data
TRDD1 missing from data
TRDD2 missing from data
TRDD3 missing from data
TRDJ1 missing from data
TRDJ2 missing from data
TRDJ3 missing from data
TRDJ4 missing from data
TRDV1 missing from data
TRDV2 missing from data
TRDV3 missing from data
TRGV9 missing from data
TRGV8 missing from data
TRGV5 missing from data
TRGV4 missing from data
TRGV3 missing from data
TRGV2 missing from data
TRGJP2 missing from data
TRGJP1 missing from data
TRGJP missing from data
TRGJ2 missing from data
TRGJ1 missing from data
TRGC2 missing from data
TRGC1 missing from data
TRAV6 missing from data
IL11RB missing from data
IL13RA2 missing from data
IL15RB missing from data
IL1RL2 missing from data
IL20RA missing from data
IL22RA1 missing from data
IL22RA2 missing from data
IL28RA missing from data
IL3RA missing from data
IL7R missing from data
IL8RA missing from data
IL8RB missing from data
IL9R missing from data
ST2 missing from data
IFNA10 missing from data
IFNA13 missing from data
IFNA14 missing from data
IFNA16 missing from data
IFNA17 missing from data
IFNA2 missing from data
IFNA21 missing from data
IFNA4 missing from data
IFNA5 missing from data
IFNA6 missing from data
IFNA7 missing from data
IFNA8 missing from data
IFNB1 missing from data
IFNE missing from data
IFNW1 missing from data
CCL1 missing from data
CCL11 missing from data
CCL13 missing from data
CCL14 missing from data
CCL14-CCL15 missing from data
CCL15 missing from data
CCL16 missing from data
CCL17 missing from data
CCL18 missing from data
CCL19 missing from data
CCL20 missing from data
CCL21 missing from data
CCL22 missing from data
CCL23 missing from data
CCL24 missing from data
CCL25 missing from data
CCL26 missing from data
CCL3L1 missing from data
CCL3L2 missing from data
CCL3L3 missing from data
CCL4L1 missing from data
CCL4L2 missing from data
CCL7 missing from data
CMA1 missing from data
CX3CL1 missing from data
CXCL12 missing from data
CXCL13 missing from data
CXCL14 missing from data
CXCL17 missing from data
CXCL6 missing from data
CYR61 missing from data
DEFA1 missing from data
DEFA3 missing from data
DEFA5 missing from data
DEFB1 missing from data
DEFB103A missing from data
DEFB104A missing from data
DEFB4 missing from data
EDN2 missing from data
EDN3 missing from data
FGF10 missing from data
HTN3 missing from data
LECT2 missing from data
PF4 missing from data
PPBP missing from data
PPBPL1 missing from data
SAA1 missing from data
SAA2 missing from data
SEMA3B missing from data
SEMA3F missing from data
SEMA5B missing from data
SEMA6B missing from data
SEMA6D missing from data
SLIT2 missing from data
0.834635592562
Abx (296, 48) 0.196565872463 -1.61326392152e-09
0.568033570064
Agprocess (102, 48) 0.165740437853 3.1646325719e-08
0.4007606543
BCRsig (61, 48) 0.171540807603 -4.6760870294e-08
0.806212978504
Cmkn (48, 48) 0.191762018858 -4.72578957211e-09
0.902707019547
CmknR (38, 48) 0.31078267515 4.93107485198e-08
0.716884837878
IFN (2, 48) 0.63549798699 -2.02505383085e-07
-0.922352708113
IFNR (3, 48) 0.799343498766 9.95016752139e-08
0.715099799498
IL (21, 48) 0.375591761545 -1.13973101184e-08
0.602312720023
ILR (29, 48) 0.209712210199 4.64108898309e-10
0.838045893304
Nkcyto (98, 48) 0.182781770595 -3.1912971826e-08
-0.0791099363552
TCRsig (85, 48) 0.16222844474 1.67985328246e-08
-0.727654169644
TGFb (13, 48) 0.286517141761 2.43322311462e-08
0.0734644489368
TGFbR (10, 48) 0.342204407932 -7.47013036953e-08
0.6069672756
TNF (11, 48) 0.350814824083 -5.57580661726e-08
0.69446207969
TNFR (18, 48) 0.290519312024 -1.37399724564e-08
Environment variable DAVID_EMAIL is not set
downloading precomputed results from S3
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set001.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set002.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set003.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set004.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set005.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set006.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set007.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set008.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set009.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set010.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set011.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set012.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set013.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set014.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set015.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set016.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set017.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set018.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set019.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set020.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set021.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set022.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set023.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set024.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set025.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set026.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set027.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set028.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set029.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set030.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set031.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set032.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set033.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set034.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set035.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set036.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set037.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set038.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set039.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set040.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set041.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set042.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set043.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set044.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set045.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set046.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set047.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set048.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set049.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set050.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set051.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set052.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set053.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set054.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set055.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set056.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set057.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set058.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set059.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set060.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set061.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set062.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_GO_set063.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set001.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set002.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set003.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set004.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set005.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set006.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set007.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set008.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set009.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set010.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set011.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set012.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set013.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set014.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set015.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set016.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set017.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set018.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set019.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set020.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set021.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set022.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set023.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set024.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set025.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set026.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set027.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set028.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set029.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set030.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set031.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set032.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set033.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set034.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set035.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set036.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set037.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set038.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set039.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set040.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set041.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set042.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set043.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set044.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set045.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set046.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set047.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set048.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set049.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set050.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set051.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set052.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set053.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set054.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set055.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set056.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set057.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set058.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set059.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set060.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set061.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set062.txt
downloading rna-seq/WGCNA/DAVID_thr8_prefilt_rin3PCreg_path_set063.txt
mean correlation: 0.808528496288
myc>sny
H3F3C
PIPSL
CCDC85B
LIME1
PPDPF
ATP5D
C9orf16
GLUD2
HLA-H
UQCRBP1
TMUB1
TMEM160
HSPB1
EIF5AL1
GZMM
CDA
CCDC124
SCAND1
HLA-G
SCAF1

sny>myc
PANK3
PDE5A
EFCAB13
CD109
STON2
HEMGN
PSMC1
C15orf54
TTN
RALGAPA1
DNM3
KCNQ1OT1
NAIP
GOLGA8S
ANXA3
CCDC144B
SCARNA2
HIST1H1E
HIST1H1D
RNU12