ArrayExpressHTS 1.9.2
Angela Goncalves , Andrew Tikhonov
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ArrayExpressHTS | | Last Changed Rev: 70419 / Revision: 74774 | | Last Changed Date: 2012-10-11 09:58:19 -0700 (Thu, 11 Oct 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ArrayExpressHTS.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayExpressHTS/DESCRIPTION’ ... OK
* this is package ‘ArrayExpressHTS’ version ‘1.9.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ArrayExpressHTS’ can be installed ... [44s/44s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cleanupCluster: no visible global function definition for
‘cleanupClusters’
prepareCluster: no visible global function definition for
‘mergeClusters’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [21s/22s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There was 1 note.
See
‘/home/biocbuild/bbs-2.12-bioc/meat/ArrayExpressHTS.Rcheck/00check.log’
for details.
* installing *source* package ‘ArrayExpressHTS’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c addXS.c -o addXS.o
addXS.c: In function ‘addXS’:
addXS.c:42:5: warning: implicit declaration of function ‘Rprintf’ [-Wimplicit-function-declaration]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c fltbam.c -o fltbam.o
fltbam.c: In function ‘equalkeys’:
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 2 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 2 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 2 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:40:5: warning: pointer targets in passing argument 2 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
fltbam.c:40:5: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c: In function ‘print_key’:
fltbam.c:45:5: warning: implicit declaration of function ‘Rprintf’ [-Wimplicit-function-declaration]
fltbam.c: In function ‘fltbam’:
fltbam.c:91:9: warning: implicit declaration of function ‘Rf_error’ [-Wimplicit-function-declaration]
fltbam.c:125:17: warning: pointer targets in passing argument 1 of ‘strcpy’ differ in signedness [-Wpointer-sign]
/usr/include/x86_64-linux-gnu/bits/string3.h:103:1: note: expected ‘char * restrict’ but argument is of type ‘unsigned char *’
fltbam.c:126:17: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
/usr/include/string.h:399:15: note: expected ‘const char *’ but argument is of type ‘unsigned char *’
fltbam.c:96:21: warning: variable ‘kk’ set but not used [-Wunused-but-set-variable]
fltbam.c: At top level:
hashtable_itr.h:46:1: warning: inline function ‘hashtable_iterator_value’ declared but never defined [enabled by default]
hashtable_itr.h:32:1: warning: inline function ‘hashtable_iterator_key’ declared but never defined [enabled by default]
hashtable_itr.h:46:1: warning: inline function ‘hashtable_iterator_value’ declared but never defined [enabled by default]
hashtable_itr.h:32:1: warning: inline function ‘hashtable_iterator_key’ declared but never defined [enabled by default]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c functions.c -o functions.o
functions.c: In function ‘checkQuality’:
functions.c:68:18: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
functions.c:69:18: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
functions.c:70:18: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
functions.c:71:18: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
functions.c: In function ‘getReadLength’:
functions.c:29:14: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
functions.c:30:14: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c hashtable.c -o hashtable.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c hashtable_itr.c -o hashtable_itr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c hashtable_utility.c -o hashtable_utility.o
gcc -std=gnu99 -shared -L/usr/local/lib -o ArrayExpressHTS.so addXS.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o /home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/ArrayExpressHTS.Rcheck/ArrayExpressHTS/libs
** R
** inst
** preparing package for lazy loading
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
** help
*** installing help indices
** building package indices
** installing vignettes
‘ArrayExpressHTS.Rnw’
** testing if installed package can be loaded
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Mon Mar 25 00:05:13 2013 [AEHTS] Setting Options Step 1
Mon Mar 25 00:05:13 2013 [AEHTS] Setting Options Step 2
Mon Mar 25 00:05:13 2013 [AEHTS] Setting Options Step 3
Mon Mar 25 00:05:13 2013 [AEHTS] Found /usr/bin/fasta_formatter
Mon Mar 25 00:05:13 2013 [AEHTS] *** WARNING ***
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] /usr/bin doesn't match to /ebi/microarray/home/biocep/local/tools/fastx-toolkit-0.0.13 defined in the 'ArrayExpressHTS.fasta_formatter' option
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] *** WARNING ***
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] cufflinks not found
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Mon Mar 25 00:05:13 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] *** WARNING ***
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] samtools not found
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Mon Mar 25 00:05:13 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] *** WARNING ***
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] bwa not found
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Mon Mar 25 00:05:13 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] *** WARNING ***
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] mmseq not found
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Mon Mar 25 00:05:13 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] *** WARNING ***
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] bam2hits not found
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Mon Mar 25 00:05:13 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] *** WARNING ***
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] bowtie not found
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Mon Mar 25 00:05:13 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] *** WARNING ***
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] tophat not found
Mon Mar 25 00:05:13 2013 [AEHTS]
Mon Mar 25 00:05:13 2013 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Mon Mar 25 00:05:13 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 00:05:13 2013 [AEHTS]
* DONE (ArrayExpressHTS)