ArrayExpressHTS 1.18.0
Angela Goncalves , Andrew Tikhonov
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/ArrayExpressHTS | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ArrayExpressHTS_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/ArrayExpressHTS.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayExpressHTS/DESCRIPTION’ ... OK
* this is package ‘ArrayExpressHTS’ version ‘1.18.0’
* 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 ... [32s/33s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
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 loading without being on the library search path ... 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’ ‘getPipelineOption’
‘processOneProjectAlignment’ ‘processOneProjectAlnReport’
‘processOneProjectEstimation’ ‘processOneProjectRawReport’
‘setProjectData’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Thu Oct 8 21:32:58 2015 [AEHTS] Setting Options Step 1
Thu Oct 8 21:32:58 2015 [AEHTS] Setting Options Step 2
Thu Oct 8 21:32:58 2015 [AEHTS] Setting Options Step 3
Thu Oct 8 21:32:58 2015 [AEHTS] *** WARNING ***
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] fasta_formatter not found
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Thu Oct 8 21:32:58 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] *** WARNING ***
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] cufflinks not found
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Thu Oct 8 21:32:58 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] *** WARNING ***
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] samtools not found
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Thu Oct 8 21:32:58 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] *** WARNING ***
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] bwa not found
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Thu Oct 8 21:32:58 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] *** WARNING ***
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] mmseq not found
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Thu Oct 8 21:32:58 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] *** WARNING ***
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] bam2hits not found
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Thu Oct 8 21:32:58 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] *** WARNING ***
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] bowtie not found
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Thu Oct 8 21:32:58 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] *** WARNING ***
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] tophat not found
Thu Oct 8 21:32:58 2015 [AEHTS]
Thu Oct 8 21:32:58 2015 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Thu Oct 8 21:32:58 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 8 21:32:58 2015 [AEHTS]
calculate_dustyScore: no visible global function definition for
‘srswor’
cleanupCluster: no visible global function definition for ‘stopCluster’
cleanupCluster: no visible global function definition for
‘cleanupClusters’
createServerLog: no visible global function definition for
‘sinkWorkerOutput’
cufflinks_to_granges: no visible global function definition for ‘Rle’
fastq_to_shortreadq: no visible global function definition for ‘subseq’
make_indexes_old: no visible global function definition for ‘subseq’
plot_readoccurence_cdf: no visible global function definition for
‘srswor’
prepareCluster: no visible global function definition for ‘makeCluster’
prepareCluster: no visible global function definition for
‘mergeClusters’
prepareCluster: no visible global function definition for
‘clusterApply’
prepareCluster: no visible global function definition for
‘clusterEvalQ’
readSDRF: no visible global function definition for
‘read.AnnotatedDataFrame’
runProjects: no visible global function definition for ‘clusterApply’
runProjects: no visible global function definition for ‘clusterEvalQ’
runProjects: no visible global function definition for ‘clusterApplyLB’
* 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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [15s/15s] 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
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/ArrayExpressHTS.Rcheck/00check.log’
for details.
* installing *source* package ‘ArrayExpressHTS’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c addXS.c -o addXS.o
addXS.c: In function ‘addXS’:
addXS.c:42: warning: implicit declaration of function ‘Rprintf’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c fltbam.c -o fltbam.o
fltbam.c: In function ‘equalkeys’:
fltbam.c:40: warning: pointer targets in passing argument 1 of ‘strcmp’ differ in signedness
fltbam.c:40: warning: pointer targets in passing argument 2 of ‘strcmp’ differ in signedness
fltbam.c: In function ‘print_key’:
fltbam.c:45: warning: implicit declaration of function ‘Rprintf’
fltbam.c: In function ‘fltbam’:
fltbam.c:91: warning: implicit declaration of function ‘Rf_error’
fltbam.c:125: warning: pointer targets in passing argument 1 of ‘__builtin___strcpy_chk’ differ in signedness
fltbam.c:125: warning: pointer targets in passing argument 1 of ‘__inline_strcpy_chk’ differ in signedness
fltbam.c:126: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
fltbam.c: At top level:
hashtable_itr.h:46: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_itr.h:32: warning: inline function ‘hashtable_iterator_key’ declared but never defined
hashtable_itr.h:46: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_itr.h:32: warning: inline function ‘hashtable_iterator_key’ declared but never defined
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c functions.c -o functions.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c hashtable.c -o hashtable.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c hashtable_itr.c -o hashtable_itr.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c hashtable_utility.c -o hashtable_utility.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o ArrayExpressHTS.so addXS.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/ArrayExpressHTS.Rcheck/ArrayExpressHTS/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
No methods found in "Biobase" for requests: read.AnnotatedDataFrame
No methods found in "IRanges" for requests: Rle, subseq
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
No methods found in "Biobase" for requests: read.AnnotatedDataFrame
No methods found in "IRanges" for requests: Rle, subseq
Thu Oct 8 21:30:11 2015 [AEHTS] Setting Options Step 1
Thu Oct 8 21:30:11 2015 [AEHTS] Setting Options Step 2
Thu Oct 8 21:30:11 2015 [AEHTS] Setting Options Step 3
Thu Oct 8 21:30:11 2015 [AEHTS] *** WARNING ***
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] fasta_formatter not found
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Thu Oct 8 21:30:11 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] *** WARNING ***
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] cufflinks not found
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Thu Oct 8 21:30:11 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] *** WARNING ***
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] samtools not found
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Thu Oct 8 21:30:11 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] *** WARNING ***
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] bwa not found
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Thu Oct 8 21:30:11 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] *** WARNING ***
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] mmseq not found
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Thu Oct 8 21:30:11 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] *** WARNING ***
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] bam2hits not found
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Thu Oct 8 21:30:11 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] *** WARNING ***
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] bowtie not found
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Thu Oct 8 21:30:11 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] *** WARNING ***
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] tophat not found
Thu Oct 8 21:30:11 2015 [AEHTS]
Thu Oct 8 21:30:11 2015 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Thu Oct 8 21:30:11 2015 [AEHTS] Use .Rprofile to make options persistent.
Thu Oct 8 21:30:11 2015 [AEHTS]
* DONE (ArrayExpressHTS)