Wei Shi
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/Rsubread |
| Branch: RELEASE_3_11 |
| Last Commit: 4e999a3 |
| Last Changed Date: 2020-08-02 18:51:16 -0400 (Sun, 02 Aug 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:55:38 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE Rsubread PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1543/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rsubread 2.2.6 Wei Shi
| malbec2 | Linux (Ubuntu 18.04.4 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: 2.2.6 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings Rsubread_2.2.6.tar.gz |
| StartedAt: 2020-10-17 05:02:41 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:04:52 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 131.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rsubread.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings Rsubread_2.2.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/Rsubread.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* this is package ‘Rsubread’ version ‘2.2.6’
* 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 36.6Mb
sub-directories of 1Mb or more:
annot 28.5Mb
libs 3.4Mb
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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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 20.898 9.215 30.366
align 19.457 8.772 28.821
sublong 10.147 2.075 12.055
* 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
‘/home/biocbuild/bbs-3.11-bioc/meat/Rsubread.Rcheck/00check.log’
for details.
Rsubread.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL Rsubread ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘Rsubread’ ... ** using staged installation @@@@@ The operating system is Linux. ** libs gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c HelperFunctions.c -o HelperFunctions.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c LRMbase-index.c -o LRMbase-index.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c LRMchro-event.c -o LRMchro-event.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c LRMfile-io.c -o LRMfile-io.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c LRMhashtable.c -o LRMhashtable.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c LRMhelper.c -o LRMhelper.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c LRMseek-zlib.c -o LRMseek-zlib.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c R_wrapper.c -o R_wrapper.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c RsimReads.c -o RsimReads.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c SNPCalling.c -o SNPCalling.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c aligner.c -o aligner.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c atgcContent.c -o atgcContent.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c build-sam-index.c -o build-sam-index.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c core-bigtable.c -o core-bigtable.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c core-indel.c -o core-indel.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c core-interface-aligner.c -o core-interface-aligner.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c core-interface-subjunc.c -o core-interface-subjunc.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c core-junction.c -o core-junction.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c core.c -o core.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c detection-calls.c -o detection-calls.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c detectionCall.c -o detectionCall.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c detectionCallAnnotation.c -o detectionCallAnnotation.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c exon-algorithms.c -o exon-algorithms.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c exon-align-indel.c -o exon-align-indel.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c exon-align.c -o exon-align.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c flattenAnnotations.c -o flattenAnnotations.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c fullscan.c -o fullscan.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c fusion-align.c -o fusion-align.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c gen_rand_reads.c -o gen_rand_reads.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c gene-algorithms.c -o gene-algorithms.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c gene-value-index.c -o gene-value-index.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c hashtable.c -o hashtable.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c index-builder.c -o index-builder.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c input-blc.c -o input-blc.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c input-files.c -o input-files.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c interval_merge.c -o interval_merge.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c long-hashtable.c -o long-hashtable.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c longread-mapping.c -o longread-mapping.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c mergeVCF.c -o mergeVCF.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c processExons.c -o processExons.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c propmapped.c -o propmapped.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c qualityScores.c -o qualityScores.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c read-repair.c -o read-repair.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c readSummary.c -o readSummary.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c removeDupReads.c -o removeDupReads.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c sam2bed.c -o sam2bed.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c sambam-file.c -o sambam-file.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c seek-zlib.c -o seek-zlib.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c sorted-hashtable.c -o sorted-hashtable.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c sublog.c -o sublog.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.2.6\"" -fpic -g -O2 -Wall -c tx-unique.c -o tx-unique.o gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/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 -lz -lpthread -DMAKE_FOR_EXON -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-bioc/R/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 | 19.457 | 8.772 | 28.821 | |
| buildindex | 3.540 | 0.951 | 4.545 | |
| featureCounts | 0.000 | 0.000 | 0.001 | |
| findCommonVariants | 0 | 0 | 0 | |
| getInBuiltAnnotation | 0.496 | 0.041 | 0.795 | |
| promoterRegions | 1.751 | 0.012 | 2.676 | |
| propmapped | 20.898 | 9.215 | 30.366 | |
| qualityScores | 0.097 | 0.000 | 0.097 | |
| simReads | 0 | 0 | 0 | |
| sublong | 10.147 | 2.075 | 12.055 | |