ArrayExpressHTS 1.12.0
Angela Goncalves , Andrew Tikhonov
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/ArrayExpressHTS | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/ArrayExpressHTS.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.12.0’
* 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 ... [21s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘Rsamtools’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘sampling’ ‘snow’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘assignPipelineOptions’ ‘createServerLog’ ‘finalCountdown’
‘getPipelineOption’ ‘processOneProjectAlignment’
‘processOneProjectAlnReport’ ‘processOneProjectEstimation’
‘processOneProjectRawReport’ ‘setProjectData’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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’
readSDRF: no visible global function definition for
‘read.AnnotatedDataFrame’
* 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘ArrayExpressHTS.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [10s/10s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 4 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/ArrayExpressHTS.Rcheck/00check.log’
for details.
* installing *source* package ‘ArrayExpressHTS’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c hashtable.c -o hashtable.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c hashtable_itr.c -o hashtable_itr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-2.13-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-2.13-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-2.13-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/ArrayExpressHTS.Rcheck/ArrayExpressHTS/libs
** R
** inst
** preparing package for lazy loading
No methods found in "Biobase" for requests: read.AnnotatedDataFrame
No methods found in "IRanges" for requests: subseq
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "Biobase" for requests: read.AnnotatedDataFrame
No methods found in "IRanges" for requests: subseq
Fri Apr 4 23:34:00 2014 [AEHTS] Setting Options Step 1
Fri Apr 4 23:34:00 2014 [AEHTS] Setting Options Step 2
Fri Apr 4 23:34:00 2014 [AEHTS] Setting Options Step 3
Fri Apr 4 23:34:00 2014 [AEHTS] Found /usr/bin/fasta_formatter
Fri Apr 4 23:34:00 2014 [AEHTS] *** WARNING ***
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [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
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] *** WARNING ***
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] cufflinks not found
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Fri Apr 4 23:34:00 2014 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] *** WARNING ***
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] samtools not found
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Fri Apr 4 23:34:00 2014 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] *** WARNING ***
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] bwa not found
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Fri Apr 4 23:34:00 2014 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] *** WARNING ***
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] mmseq not found
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Fri Apr 4 23:34:00 2014 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] *** WARNING ***
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] bam2hits not found
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Fri Apr 4 23:34:00 2014 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] *** WARNING ***
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] bowtie not found
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Fri Apr 4 23:34:00 2014 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] *** WARNING ***
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] tophat not found
Fri Apr 4 23:34:00 2014 [AEHTS]
Fri Apr 4 23:34:00 2014 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Fri Apr 4 23:34:00 2014 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 4 23:34:00 2014 [AEHTS]
* DONE (ArrayExpressHTS)