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Package 44/631HostnameOS / ArchBUILDCHECKBUILD BIN
ArrayExpressHTS 1.9.2
Angela Goncalves , Andrew Tikhonov
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ArrayExpressHTS
Last Changed Rev: 70419 / Revision: 72575
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 
lamb2 Linux (openSUSE 11.4) / 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  OK  OK 

Summary

Package: ArrayExpressHTS
Version: 1.9.2
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ArrayExpressHTS_1.9.2.tar.gz
StartedAt: 2013-01-16 00:39:16 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 00:44:21 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 304.8 seconds
RetCode: 0
Status:  OK 
CheckDir: ArrayExpressHTS.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/ArrayExpressHTS.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ... 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 ... 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
  ‘/loc/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"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -c addXS.c -o addXS.o
addXS.c: In function ‘addXS’:
addXS.c:42:5: warning: implicit declaration of function ‘Rprintf’
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"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -c fltbam.c -o fltbam.o
fltbam.c: In function ‘print_key’:
fltbam.c:45:5: warning: implicit declaration of function ‘Rprintf’
fltbam.c: In function ‘fltbam’:
fltbam.c:91:9: warning: implicit declaration of function ‘Rf_error’
fltbam.c: At top level:
hashtable_itr.h:46:1: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_itr.h:32:1: warning: inline function ‘hashtable_iterator_key’ declared but never defined
hashtable_itr.h:46:1: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_itr.h:32:1: warning: inline function ‘hashtable_iterator_key’ declared but never defined
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"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -c functions.c -o functions.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"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -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"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -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"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -c hashtable_utility.c -o hashtable_utility.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o ArrayExpressHTS.so addXS.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o /loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libbam.a /loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libbcf.a /loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/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
   ‘ArrayExpressHTS.Rnw’ 
** testing if installed package can be loaded
Wed Jan 16 00:39:50 2013 [AEHTS] Setting Options Step 1
Wed Jan 16 00:39:50 2013 [AEHTS] Setting Options Step 2
Wed Jan 16 00:39:50 2013 [AEHTS] Setting Options Step 3
Wed Jan 16 00:39:50 2013 [AEHTS] *** WARNING ***
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS]     fasta_formatter not found
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Wed Jan 16 00:39:50 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS] *** WARNING ***
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS]     cufflinks not found
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Wed Jan 16 00:39:50 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS] *** WARNING ***
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS]     samtools not found
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Wed Jan 16 00:39:50 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS] *** WARNING ***
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS]     bwa not found
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Wed Jan 16 00:39:50 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS] *** WARNING ***
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS]     mmseq not found
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Wed Jan 16 00:39:50 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS] *** WARNING ***
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS]     bam2hits not found
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Wed Jan 16 00:39:50 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS] *** WARNING ***
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS]     bowtie not found
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Wed Jan 16 00:39:50 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS] *** WARNING ***
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS]     tophat not found
Wed Jan 16 00:39:50 2013 [AEHTS] 
Wed Jan 16 00:39:50 2013 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Wed Jan 16 00:39:50 2013 [AEHTS] Use .Rprofile to make options persistent.
Wed Jan 16 00:39:50 2013 [AEHTS] 

* DONE (ArrayExpressHTS)

ArrayExpressHTS.Rcheck/ArrayExpressHTS-Ex.timings:

nameusersystemelapsed
ArrayExpressHTS0.0360.0000.036
ArrayExpressHTSFastQ0.0520.0000.051
isRCloud0.020.000.02
package-options0.0280.0040.032
prepareAnnotation0.0280.0000.027
prepareReference0.040.000.04
processing-options0.0280.0000.028