Wei Shi
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Rsubread |
| Branch: master |
| Last Commit: 8a60064 |
| Last Changed Date: 2019-04-08 01:22:04 -0400 (Mon, 08 Apr 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:00:33 -0400 (Tue, 09 Apr 2019).
| Package 1398/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rsubread 1.33.33 Wei Shi
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED... | ||||||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
| Package: Rsubread |
| Version: 1.33.33 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rsubread_1.33.33.tar.gz |
| StartedAt: 2019-04-09 05:10:18 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:11:56 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 97.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rsubread.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rsubread_1.33.33.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Rsubread.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* this is package ‘Rsubread’ version ‘1.33.33’
* 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 ‘Rsubread’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 34.0Mb
sub-directories of 1Mb or more:
annot 28.5Mb
qualf 3.4Mb
* checking package directory ... OK
* checking ‘build’ 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 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 ... OK
* 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 shell scripts ... 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
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sublong 15.917 6.967 21.092
align 7.775 6.116 14.091
propmapped 7.748 5.906 14.517
buildindex 5.991 3.459 9.529
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/Rsubread.Rcheck/00check.log’
for details.
Rsubread.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rsubread ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘Rsubread’ ... ** using staged installation @@@@@ The operating system is Darwin. ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c HelperFunctions.c -o HelperFunctions.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c LRMbase-index.c -o LRMbase-index.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c LRMchro-event.c -o LRMchro-event.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c LRMfile-io.c -o LRMfile-io.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c LRMhashtable.c -o LRMhashtable.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c LRMhelper.c -o LRMhelper.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c LRMseek-zlib.c -o LRMseek-zlib.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c R_wrapper.c -o R_wrapper.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c RsimReads.c -o RsimReads.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c SNPCalling.c -o SNPCalling.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c aligner.c -o aligner.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c atgcContent.c -o atgcContent.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c build-sam-index.c -o build-sam-index.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c core-bigtable.c -o core-bigtable.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c core-indel.c -o core-indel.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c core-interface-aligner.c -o core-interface-aligner.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c core-interface-subjunc.c -o core-interface-subjunc.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c core-junction.c -o core-junction.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c core.c -o core.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c detection-calls.c -o detection-calls.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c detectionCall.c -o detectionCall.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c detectionCallAnnotation.c -o detectionCallAnnotation.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c exon-algorithms.c -o exon-algorithms.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c exon-align-indel.c -o exon-align-indel.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c exon-align.c -o exon-align.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c flattenAnnotations.c -o flattenAnnotations.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c fullscan.c -o fullscan.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c fusion-align.c -o fusion-align.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c gen_rand_reads.c -o gen_rand_reads.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c gene-algorithms.c -o gene-algorithms.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c gene-value-index.c -o gene-value-index.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c hashtable.c -o hashtable.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c index-builder.c -o index-builder.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c input-files.c -o input-files.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c interval_merge.c -o interval_merge.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c long-hashtable.c -o long-hashtable.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c longread-mapping.c -o longread-mapping.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c mergeVCF.c -o mergeVCF.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c processExons.c -o processExons.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c propmapped.c -o propmapped.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c qualityScores.c -o qualityScores.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c read-repair.c -o read-repair.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c readSummary.c -o readSummary.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c removeDupReads.c -o removeDupReads.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c sam2bed.c -o sam2bed.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c sambam-file.c -o sambam-file.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c seek-zlib.c -o seek-zlib.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c sorted-hashtable.c -o sorted-hashtable.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c sublog.c -o sublog.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 1.33.33\"" -fPIC -Wall -g -O2 -c tx-unique.c -o tx-unique.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 Rsubread.so HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rsubread/00new/Rsubread/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘Rsubread.Rnw’ ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rsubread)
Rsubread.Rcheck/Rsubread-Ex.timings
| name | user | system | elapsed | |
| align | 7.775 | 6.116 | 14.091 | |
| buildindex | 5.991 | 3.459 | 9.529 | |
| featureCounts | 0.001 | 0.001 | 0.001 | |
| findCommonVariants | 0.000 | 0.000 | 0.001 | |
| getInBuiltAnnotation | 0.475 | 0.053 | 0.555 | |
| promoterRegions | 1.465 | 0.111 | 1.690 | |
| propmapped | 7.748 | 5.906 | 14.517 | |
| qualityScores | 0.086 | 0.034 | 0.121 | |
| simReads | 0.001 | 0.000 | 0.000 | |
| sublong | 15.917 | 6.967 | 21.092 | |