Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:51 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the Rsubread package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rsubread.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1639/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rsubread 2.6.4 (landing page) Wei Shi
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: Rsubread |
Version: 2.6.4 |
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_2.6.4.tar.gz |
StartedAt: 2021-10-14 23:26:09 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 23:28:26 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 137.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Rsubread.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_2.6.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/Rsubread.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Rsubread/DESCRIPTION’ ... OK * this is package ‘Rsubread’ version ‘2.6.4’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 34.4Mb sub-directories of 1Mb or more: annot 28.5Mb libs 1.0Mb 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 ... NOTE .extract.sample.table.cols: no visible global function definition for ‘median’ Undefined global functions or variables: median Consider adding importFrom("stats", "median") to your NAMESPACE file. * 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 use of PKG_*FLAGS in Makefiles ... 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 (user + system) or elapsed time > 5s user system elapsed propmapped 21.161 2.892 24.320 align 21.276 2.637 24.266 sublong 15.275 3.258 17.680 buildindex 6.606 1.881 8.618 * 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-3.13-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/4.1/Resources/library’ * installing *source* package ‘Rsubread’ ... ** using staged installation @@@@@ The operating system is Darwin. ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c HelperFunctions.c -o HelperFunctions.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c LRMbase-index.c -o LRMbase-index.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c LRMchro-event.c -o LRMchro-event.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c LRMfile-io.c -o LRMfile-io.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c LRMhashtable.c -o LRMhashtable.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c LRMhelper.c -o LRMhelper.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c LRMseek-zlib.c -o LRMseek-zlib.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c R_wrapper.c -o R_wrapper.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c RsimReads.c -o RsimReads.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c SNPCalling.c -o SNPCalling.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c aligner.c -o aligner.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c atgcContent.c -o atgcContent.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c build-sam-index.c -o build-sam-index.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c core-bigtable.c -o core-bigtable.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c core-indel.c -o core-indel.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c core-interface-aligner.c -o core-interface-aligner.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c core-interface-subjunc.c -o core-interface-subjunc.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c core-junction.c -o core-junction.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c core.c -o core.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c detection-calls.c -o detection-calls.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c detectionCall.c -o detectionCall.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c detectionCallAnnotation.c -o detectionCallAnnotation.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c exon-algorithms.c -o exon-algorithms.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c exon-align-indel.c -o exon-align-indel.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c exon-align.c -o exon-align.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c flattenAnnotations.c -o flattenAnnotations.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c fullscan.c -o fullscan.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c fusion-align.c -o fusion-align.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c gen_rand_reads.c -o gen_rand_reads.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c gene-algorithms.c -o gene-algorithms.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c gene-value-index.c -o gene-value-index.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c hashtable.c -o hashtable.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c index-builder.c -o index-builder.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c input-blc.c -o input-blc.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c input-files.c -o input-files.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c interval_merge.c -o interval_merge.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c long-hashtable.c -o long-hashtable.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c longread-mapping.c -o longread-mapping.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c mergeVCF.c -o mergeVCF.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c processExons.c -o processExons.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c propmapped.c -o propmapped.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c qualityScores.c -o qualityScores.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c read-repair.c -o read-repair.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c readSummary.c -o readSummary.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c removeDupReads.c -o removeDupReads.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c sam2bed.c -o sam2bed.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c sambam-file.c -o sambam-file.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c seek-zlib.c -o seek-zlib.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c sorted-hashtable.c -o sorted-hashtable.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c sublog.c -o sublog.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.6.4\"" -fPIC -Wall -g -O2 -c tx-unique.c -o tx-unique.o clang -mmacosx-version-min=10.13 -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-blc.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/4.1/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 | 21.276 | 2.637 | 24.266 | |
buildindex | 6.606 | 1.881 | 8.618 | |
featureCounts | 0.000 | 0.001 | 0.002 | |
findCommonVariants | 0 | 0 | 0 | |
getInBuiltAnnotation | 0.408 | 0.022 | 0.431 | |
promoterRegions | 1.283 | 0.035 | 1.318 | |
propmapped | 21.161 | 2.892 | 24.320 | |
qualityScores | 0.061 | 0.007 | 0.069 | |
simReads | 0 | 0 | 0 | |
sublong | 15.275 | 3.258 | 17.680 | |