Wei Shi
| Snapshot Date: 2025-01-24 13:40 -0500 (Fri, 24 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/Rsubread |
| git_branch: devel |
| git_last_commit: ce7af90 |
| git_last_commit_date: 2025-01-12 16:35:03 -0500 (Sun, 12 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-25 15:37 -0500 (Sat, 25 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4658 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4455 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1802/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rsubread 2.21.1 (landing page) Wei Shi
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the Rsubread package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: Rsubread |
| Version: 2.21.1 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Rsubread_2.21.1.tar.gz |
| StartedAt: 2025-01-25 02:00:44 -0500 (Sat, 25 Jan 2025) |
| EndedAt: 2025-01-25 02:11:48 -0500 (Sat, 25 Jan 2025) |
| EllapsedTime: 664.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Rsubread.Rcheck |
| Warnings: 2 |
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### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Rsubread_2.21.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Rsubread.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* this is package ‘Rsubread’ version ‘2.21.1’
* 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 ... WARNING
Found the following significant warnings:
hashtable.c:51:76: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
readSummary.c:858:47: warning: format ‘%s’ expects argument of type ‘char *’, but argument 5 has type ‘void *’ [-Wformat=]
See ‘/home/biocbuild/bbs-3.21-bioc/meat/Rsubread.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
installed size is 22.7Mb
sub-directories of 1Mb or more:
annot 16.5Mb
libs 2.4Mb
qualf 2.3Mb
* 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 code 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 ... 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/Rsubread/libs/Rsubread.so’:
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘stderr’, possibly from ‘stderr’ (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 nor [v]sprintf. 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 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 28.403 20.576 49.021
align 25.427 20.293 45.843
sublong 20.577 7.450 27.957
buildindex 7.852 2.544 10.460
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/Rsubread.Rcheck/00check.log’
for details.
Rsubread.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Rsubread
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘Rsubread’ ...
** this is package ‘Rsubread’ version ‘2.21.1’
** using staged installation
@@@@@ The operating system is Linux.
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c HelperFunctions.c -o HelperFunctions.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c LRMbase-index.c -o LRMbase-index.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c LRMchro-event.c -o LRMchro-event.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c LRMfile-io.c -o LRMfile-io.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c LRMhashtable.c -o LRMhashtable.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c LRMhelper.c -o LRMhelper.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c R_wrapper.c -o R_wrapper.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c RsimReads.c -o RsimReads.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c SNPCalling.c -o SNPCalling.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c aligner.c -o aligner.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c atgcContent.c -o atgcContent.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c build-sam-index.c -o build-sam-index.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c cell-counts.c -o cell-counts.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c core-bigtable.c -o core-bigtable.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c core-indel.c -o core-indel.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c core-interface-aligner.c -o core-interface-aligner.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c core-junction.c -o core-junction.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c core.c -o core.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c detection-calls.c -o detection-calls.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c detectionCall.c -o detectionCall.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c exon-algorithms.c -o exon-algorithms.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c exon-align-indel.c -o exon-align-indel.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c exon-align.c -o exon-align.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c flattenAnnotations.c -o flattenAnnotations.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c fullscan.c -o fullscan.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c fusion-align.c -o fusion-align.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c gen_rand_reads.c -o gen_rand_reads.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c gene-algorithms.c -o gene-algorithms.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c gene-value-index.c -o gene-value-index.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c hashtable.c -o hashtable.o
hashtable.c: In function ‘ArrayListStringJoin’:
hashtable.c:51:76: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
51 | outpt += snprintf(outbuf + outpt, out_max_len - outpt -1,"%s%s", list->elementList [ x1 ], x1<list->numOfElements-1?",":"");
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| char * void *
| %p
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c index-builder.c -o index-builder.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c input-blc.c -o input-blc.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c input-files.c -o input-files.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c interval_merge.c -o interval_merge.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c long-hashtable.c -o long-hashtable.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c longread-mapping.c -o longread-mapping.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c mergeVCF.c -o mergeVCF.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c processExons.c -o processExons.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c propmapped.c -o propmapped.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c qualityScores.c -o qualityScores.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c read-repair.c -o read-repair.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c readSummary.c -o readSummary.o
readSummary.c: In function ‘sort_junc_feature_make_gaps’:
readSummary.c:858:47: warning: format ‘%s’ expects argument of type ‘char *’, but argument 5 has type ‘void *’ [-Wformat=]
858 | fprintf(stderr,"POS %d %d of %s\n", min_start,max_stop,k);
| ~^ ~
| | |
| char * void *
| %p
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c removeDupReads.c -o removeDupReads.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c sam2bed.c -o sam2bed.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c sambam-file.c -o sambam-file.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c seek-zlib.c -o seek-zlib.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c sorted-hashtable.c -o sorted-hashtable.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c sublog.c -o sublog.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -c tx-unique.c -o tx-unique.o
gcc -shared -L/home/biocbuild/bbs-3.21-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 cell-counts.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-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-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
** 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 | 25.427 | 20.293 | 45.843 | |
| buildindex | 7.852 | 2.544 | 10.460 | |
| cellCounts | 0 | 0 | 0 | |
| featureCounts | 0 | 0 | 0 | |
| findCommonVariants | 0 | 0 | 0 | |
| getInBuiltAnnotation | 0.321 | 0.077 | 0.399 | |
| promoterRegions | 1.698 | 0.085 | 1.783 | |
| propmapped | 28.403 | 20.576 | 49.021 | |
| qualityScores | 0.037 | 0.004 | 0.041 | |
| simReads | 0 | 0 | 0 | |
| sublong | 20.577 | 7.450 | 27.957 | |