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BioC 2.12: CHECK report for ArrayExpressHTS on george2

This page was generated on 2013-10-09 09:37:44 -0700 (Wed, 09 Oct 2013).

Package 46/671HostnameOS / ArchBUILDCHECKBUILD BIN
ArrayExpressHTS 1.10.0
Angela Goncalves , Andrew Tikhonov
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/ArrayExpressHTS
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
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 Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: ArrayExpressHTS
Version: 1.10.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ArrayExpressHTS_1.10.0.tar.gz
StartedAt: 2013-10-09 00:10:26 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 00:17:32 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 426.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ArrayExpressHTS.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ArrayExpressHTS.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.10.0’
* 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 ... [42s/42s] 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 ... [22s/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.

ArrayExpressHTS.Rcheck/00install.out:

* 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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Wed Oct  9 00:11:09 2013 [AEHTS] Setting Options Step 1
Wed Oct  9 00:11:09 2013 [AEHTS] Setting Options Step 2
Wed Oct  9 00:11:09 2013 [AEHTS] Setting Options Step 3
Wed Oct  9 00:11:09 2013 [AEHTS] Found /usr/bin/fasta_formatter
Wed Oct  9 00:11:09 2013 [AEHTS] *** WARNING ***
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 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
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS] *** WARNING ***
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS]     cufflinks not found
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Wed Oct  9 00:11:09 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS] *** WARNING ***
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS]     samtools not found
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Wed Oct  9 00:11:09 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS] *** WARNING ***
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS]     bwa not found
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Wed Oct  9 00:11:09 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS] *** WARNING ***
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS]     mmseq not found
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Wed Oct  9 00:11:09 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS] *** WARNING ***
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS]     bam2hits not found
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Wed Oct  9 00:11:09 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS] *** WARNING ***
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS]     bowtie not found
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Wed Oct  9 00:11:09 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS] *** WARNING ***
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS]     tophat not found
Wed Oct  9 00:11:09 2013 [AEHTS] 
Wed Oct  9 00:11:09 2013 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Wed Oct  9 00:11:09 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed Oct  9 00:11:09 2013 [AEHTS] 
* DONE (ArrayExpressHTS)

ArrayExpressHTS.Rcheck/ArrayExpressHTS-Ex.timings:

nameusersystemelapsed
ArrayExpressHTS0.7160.0880.842
ArrayExpressHTSFastQ0.0880.0080.098
isRCloud0.0240.0000.022
package-options0.0400.0000.039
prepareAnnotation0.0560.0080.062
prepareReference0.0320.0000.032
processing-options0.0200.0000.022