Wei Shi
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/Rsubread |
| git_branch: RELEASE_3_15 |
| git_last_commit: 5c2d59e |
| git_last_commit_date: 2022-08-12 16:21:12 -0400 (Fri, 12 Aug 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:23:38 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1711/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rsubread 2.10.5 (landing page) Wei Shi
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Rsubread |
| Version: 2.10.5 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rsubread_2.10.5.tar.gz |
| StartedAt: 2022-10-19 07:24:27 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 07:30:53 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 385.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rsubread.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rsubread_2.10.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/Rsubread.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘2.10.5’
* 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 36.8Mb
sub-directories of 1Mb or more:
annot 30.9Mb
libs 1.1Mb
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 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 86.861 9.593 96.740
align 87.211 9.112 96.658
sublong 60.438 8.862 68.607
buildindex 24.557 5.464 30.182
* 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-3.15-bioc/meat/Rsubread.Rcheck/00check.log’
for details.
Rsubread.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rsubread
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -fPIC -Wall -g -O2 -c cell-counts.c -o cell-counts.o
cell-counts.c:4213:10: warning: unused variable 'tv2' [-Wunused-variable]
void ** tv2 = me->appendix3;
^
1 warning generated.
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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 2.10.5\"" -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 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 -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/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
** 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 | 87.211 | 9.112 | 96.658 | |
| buildindex | 24.557 | 5.464 | 30.182 | |
| cellCounts | 0 | 0 | 0 | |
| featureCounts | 0.000 | 0.000 | 0.001 | |
| findCommonVariants | 0 | 0 | 0 | |
| getInBuiltAnnotation | 0.573 | 0.031 | 0.607 | |
| promoterRegions | 3.000 | 0.057 | 3.081 | |
| propmapped | 86.861 | 9.593 | 96.740 | |
| qualityScores | 0.081 | 0.004 | 0.086 | |
| simReads | 0.001 | 0.000 | 0.001 | |
| sublong | 60.438 | 8.862 | 68.607 | |