ArrayExpressHTS 1.24.0
Angela Goncalves , Andrew Tikhonov
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ArrayExpressHTS | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| 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_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ArrayExpressHTS.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayExpressHTS/DESCRIPTION’ ... OK
* this is package ‘ArrayExpressHTS’ version ‘1.24.0’
* 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 ... 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
Fri Apr 14 22:44:51 2017 [AEHTS] Setting Options Step 1
Fri Apr 14 22:44:51 2017 [AEHTS] Setting Options Step 2
Fri Apr 14 22:44:51 2017 [AEHTS] Setting Options Step 3
Fri Apr 14 22:44:51 2017 [AEHTS] *** WARNING ***
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] fasta_formatter not found
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Fri Apr 14 22:44:51 2017 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] *** WARNING ***
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] cufflinks not found
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Fri Apr 14 22:44:51 2017 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] *** WARNING ***
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] samtools not found
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Fri Apr 14 22:44:51 2017 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] *** WARNING ***
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] bwa not found
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Fri Apr 14 22:44:51 2017 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] *** WARNING ***
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] mmseq not found
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Fri Apr 14 22:44:51 2017 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] *** WARNING ***
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] bam2hits not found
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Fri Apr 14 22:44:51 2017 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] *** WARNING ***
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] bowtie not found
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Fri Apr 14 22:44:51 2017 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] *** WARNING ***
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] tophat not found
Fri Apr 14 22:44:51 2017 [AEHTS]
Fri Apr 14 22:44:51 2017 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Fri Apr 14 22:44:51 2017 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 14 22:44:51 2017 [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’
Undefined global functions or variables:
Rle cleanupClusters clusterApply clusterApplyLB clusterEvalQ
makeCluster mergeClusters read.AnnotatedDataFrame sinkWorkerOutput
srswor stopCluster subseq
* 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 ... 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-3.4-bioc/meat/ArrayExpressHTS.Rcheck/00check.log’
for details.
* installing *source* package ‘ArrayExpressHTS’ ...
** libs
clang -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/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c addXS.c -o addXS.o
addXS.c:42:5: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration]
Rprintf("What?\n");
^
1 warning generated.
clang -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/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c fltbam.c -o fltbam.o
fltbam.c:40:19: warning: passing 'unsigned char [50]' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^˜˜˜˜˜˜
/usr/include/string.h:77:25: note: passing argument to parameter here
int strcmp(const char *, const char *);
^
fltbam.c:40:28: warning: passing 'unsigned char [50]' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
return(strcmp(k1->str, k2->str) == 0);
^˜˜˜˜˜˜
/usr/include/string.h:77:39: note: passing argument to parameter here
int strcmp(const char *, const char *);
^
fltbam.c:45:5: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration]
Rprintf("ID: %s, %d\n", k->str, k->length);
^
fltbam.c:91:9: warning: implicit declaration of function 'Rf_error' is invalid in C99 [-Wimplicit-function-declaration]
Rf_error("Fail to open BAM file %s\n", argv[1]);
^
fltbam.c:125:24: warning: passing 'unsigned char [50]' to parameter of type 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
strcpy(k->str, bam1_qname(line));
^˜˜˜˜˜
/usr/include/secure/_string.h:83:27: note: expanded from macro 'strcpy'
__builtin___strcpy_chk (dest, src, __darwin_obsz (dest))
^
fltbam.c:126:36: warning: passing 'unsigned char [50]' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
k->length = strlen(k->str);
^˜˜˜˜˜
/usr/include/string.h:82:28: note: passing argument to parameter here
size_t strlen(const char *);
^
In file included from fltbam.c:4:
./hashtable_itr.h:32:1: warning: inline function 'hashtable_iterator_key' is not defined [-Wundefined-inline]
hashtable_iterator_key(struct hashtable_itr *i);
^
fltbam.c:189:18: note: used here
kk = hashtable_iterator_key(itr);
^
In file included from fltbam.c:4:
./hashtable_itr.h:46:1: warning: inline function 'hashtable_iterator_value' is not defined [-Wundefined-inline]
hashtable_iterator_value(struct hashtable_itr *i);
^
fltbam.c:190:17: note: used here
v = hashtable_iterator_value(itr);
^
8 warnings generated.
clang -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/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c functions.c -o functions.o
clang -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/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c hashtable.c -o hashtable.o
clang -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/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c hashtable_itr.c -o hashtable_itr.o
clang -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/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/include" -fPIC -Wall -mtune=core2 -g -O2 -c hashtable_utility.c -o hashtable_utility.o
clang -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 -o ArrayExpressHTS.so addXS.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/biocbuild/bbs-3.4-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: Rle, 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: Rle, subseq
Fri Apr 14 22:43:18 2017 [AEHTS] Setting Options Step 1
Fri Apr 14 22:43:18 2017 [AEHTS] Setting Options Step 2
Fri Apr 14 22:43:18 2017 [AEHTS] Setting Options Step 3
Fri Apr 14 22:43:18 2017 [AEHTS] *** WARNING ***
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] fasta_formatter not found
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Fri Apr 14 22:43:18 2017 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] *** WARNING ***
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] cufflinks not found
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Fri Apr 14 22:43:18 2017 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] *** WARNING ***
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] samtools not found
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Fri Apr 14 22:43:18 2017 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] *** WARNING ***
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] bwa not found
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Fri Apr 14 22:43:18 2017 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] *** WARNING ***
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] mmseq not found
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Fri Apr 14 22:43:18 2017 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] *** WARNING ***
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] bam2hits not found
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Fri Apr 14 22:43:18 2017 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] *** WARNING ***
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] bowtie not found
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Fri Apr 14 22:43:18 2017 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] *** WARNING ***
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] tophat not found
Fri Apr 14 22:43:18 2017 [AEHTS]
Fri Apr 14 22:43:18 2017 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Fri Apr 14 22:43:18 2017 [AEHTS] Use .Rprofile to make options persistent.
Fri Apr 14 22:43:18 2017 [AEHTS]
* DONE (ArrayExpressHTS)