Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:49:16 -0400 (Wed, 17 Oct 2018).
Package 66/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ArrayExpressHTS 1.30.0 Angela Goncalves
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED... | ||||||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: ArrayExpressHTS |
Version: 1.30.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ArrayExpressHTS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ArrayExpressHTS_1.30.0.tar.gz |
StartedAt: 2018-10-16 19:54:36 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 19:58:40 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 244.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ArrayExpressHTS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ArrayExpressHTS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ArrayExpressHTS_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ArrayExpressHTS.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ArrayExpressHTS/DESCRIPTION’ ... OK * this is package ‘ArrayExpressHTS’ version ‘1.30.0’ * 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 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 Tue Oct 16 19:56:50 2018 [AEHTS] Setting Options Step 1 Tue Oct 16 19:56:50 2018 [AEHTS] Setting Options Step 2 Tue Oct 16 19:56:50 2018 [AEHTS] Setting Options Step 3 Tue Oct 16 19:56:50 2018 [AEHTS] *** WARNING *** Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] fasta_formatter not found Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location. Tue Oct 16 19:56:50 2018 [AEHTS] Use .Rprofile to make options persistent. Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] *** WARNING *** Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] cufflinks not found Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location. Tue Oct 16 19:56:50 2018 [AEHTS] Use .Rprofile to make options persistent. Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] *** WARNING *** Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] samtools not found Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location. Tue Oct 16 19:56:50 2018 [AEHTS] Use .Rprofile to make options persistent. Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] *** WARNING *** Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] bwa not found Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location. Tue Oct 16 19:56:50 2018 [AEHTS] Use .Rprofile to make options persistent. Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] *** WARNING *** Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] mmseq not found Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location. Tue Oct 16 19:56:50 2018 [AEHTS] Use .Rprofile to make options persistent. Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] *** WARNING *** Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] bam2hits not found Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location. Tue Oct 16 19:56:50 2018 [AEHTS] Use .Rprofile to make options persistent. Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] *** WARNING *** Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] bowtie not found Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location. Tue Oct 16 19:56:50 2018 [AEHTS] Use .Rprofile to make options persistent. Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] *** WARNING *** Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] tophat not found Tue Oct 16 19:56:50 2018 [AEHTS] Tue Oct 16 19:56:50 2018 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location. Tue Oct 16 19:56:50 2018 [AEHTS] Use .Rprofile to make options persistent. Tue Oct 16 19:56:50 2018 [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 ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ArrayExpressHTS/libs/ArrayExpressHTS.so’: Found ‘___stderrp’, possibly from ‘stderr’ (C) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking sizes of PDF files under ‘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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.7-bioc/meat/ArrayExpressHTS.Rcheck/00check.log’ for details.
ArrayExpressHTS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ArrayExpressHTS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * 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"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include -fPIC -Wall -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"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include -fPIC -Wall -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"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include -fPIC -Wall -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"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include -fPIC -Wall -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"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include -fPIC -Wall -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"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include -fPIC -Wall -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/3.5/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument] installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ArrayExpressHTS/libs ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘Biobase’ for request: ‘read.AnnotatedDataFrame’ when loading ‘ArrayExpressHTS’ No methods found in package ‘IRanges’ for requests: ‘Rle’, ‘subseq’ when loading ‘ArrayExpressHTS’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded No methods found in package ‘Biobase’ for request: ‘read.AnnotatedDataFrame’ when loading ‘ArrayExpressHTS’ No methods found in package ‘IRanges’ for requests: ‘Rle’, ‘subseq’ when loading ‘ArrayExpressHTS’ Tue Oct 16 16:06:14 2018 [AEHTS] Setting Options Step 1 Tue Oct 16 16:06:14 2018 [AEHTS] Setting Options Step 2 Tue Oct 16 16:06:14 2018 [AEHTS] Setting Options Step 3 Tue Oct 16 16:06:14 2018 [AEHTS] *** WARNING *** Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] fasta_formatter not found Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location. Tue Oct 16 16:06:14 2018 [AEHTS] Use .Rprofile to make options persistent. Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] *** WARNING *** Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] cufflinks not found Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location. Tue Oct 16 16:06:14 2018 [AEHTS] Use .Rprofile to make options persistent. Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] *** WARNING *** Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] samtools not found Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location. Tue Oct 16 16:06:14 2018 [AEHTS] Use .Rprofile to make options persistent. Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] *** WARNING *** Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] bwa not found Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location. Tue Oct 16 16:06:14 2018 [AEHTS] Use .Rprofile to make options persistent. Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] *** WARNING *** Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] mmseq not found Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location. Tue Oct 16 16:06:14 2018 [AEHTS] Use .Rprofile to make options persistent. Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] *** WARNING *** Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] bam2hits not found Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location. Tue Oct 16 16:06:14 2018 [AEHTS] Use .Rprofile to make options persistent. Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] *** WARNING *** Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] bowtie not found Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location. Tue Oct 16 16:06:14 2018 [AEHTS] Use .Rprofile to make options persistent. Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] *** WARNING *** Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] tophat not found Tue Oct 16 16:06:14 2018 [AEHTS] Tue Oct 16 16:06:14 2018 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location. Tue Oct 16 16:06:14 2018 [AEHTS] Use .Rprofile to make options persistent. Tue Oct 16 16:06:14 2018 [AEHTS] * DONE (ArrayExpressHTS)
ArrayExpressHTS.Rcheck/ArrayExpressHTS-Ex.timings
name | user | system | elapsed | |
ArrayExpressHTS | 0.006 | 0.000 | 0.006 | |
ArrayExpressHTSFastQ | 0.011 | 0.001 | 0.011 | |
isRCloud | 0.003 | 0.000 | 0.003 | |
package-options | 0.004 | 0.000 | 0.004 | |
prepareAnnotation | 0.005 | 0.001 | 0.005 | |
prepareReference | 0.006 | 0.001 | 0.006 | |
processing-options | 0.002 | 0.000 | 0.002 | |