Wei Shi
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/Rsubread |
| git_branch: RELEASE_3_16 |
| git_last_commit: fef44d1 |
| git_last_commit_date: 2023-03-01 13:56:53 -0400 (Wed, 01 Mar 2023) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:50 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 1737/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rsubread 2.12.3 (landing page) Wei Shi
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Rsubread |
| Version: 2.12.3 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rsubread.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings Rsubread_2.12.3.tar.gz |
| StartedAt: 2023-04-11 05:29:40 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 05:32:34 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 174.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rsubread.Rcheck |
| Warnings: 0 |
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### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rsubread.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings Rsubread_2.12.3.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/Rsubread.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Rsubread/DESCRIPTION' ... OK
* this is package 'Rsubread' version '2.12.3'
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/Rsubread/libs/x64/Rsubread.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
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. 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 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
align 29.14 3.50 32.74
propmapped 27.64 4.19 32.50
sublong 24.23 4.62 28.52
buildindex 10.08 1.92 12.03
* 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
'F:/biocbuild/bbs-3.16-bioc/meat/Rsubread.Rcheck/00check.log'
for details.
Rsubread.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL Rsubread
###
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* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'Rsubread' ...
** using staged installation
@@@@@ The operating system is Windows.
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c HelperFunctions.c -o HelperFunctions.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMbase-index.c -o LRMbase-index.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMchro-event.c -o LRMchro-event.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMfile-io.c -o LRMfile-io.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhashtable.c -o LRMhashtable.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhelper.c -o LRMhelper.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_wrapper.c -o R_wrapper.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RsimReads.c -o RsimReads.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SNPCalling.c -o SNPCalling.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c aligner.c -o aligner.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c atgcContent.c -o atgcContent.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c build-sam-index.c -o build-sam-index.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c cell-counts.c -o cell-counts.o
cell-counts.c: In function 'cellCounts_find_hits_for_mapped_section':
cell-counts.c:1606:5: warning: 'search_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
1606 | if(search_start>0xffffff00) return;
| ^
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-bigtable.c -o core-bigtable.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-indel.c -o core-indel.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-aligner.c -o core-interface-aligner.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-junction.c -o core-junction.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core.c -o core.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detection-calls.c -o detection-calls.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCall.c -o detectionCall.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-algorithms.c -o exon-algorithms.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align-indel.c -o exon-align-indel.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align.c -o exon-align.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c flattenAnnotations.c -o flattenAnnotations.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fullscan.c -o fullscan.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fusion-align.c -o fusion-align.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gen_rand_reads.c -o gen_rand_reads.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-algorithms.c -o gene-algorithms.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-value-index.c -o gene-value-index.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hashtable.c -o hashtable.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c index-builder.c -o index-builder.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-blc.c -o input-blc.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-files.c -o input-files.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c interval_merge.c -o interval_merge.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c long-hashtable.c -o long-hashtable.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c longread-mapping.c -o longread-mapping.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mergeVCF.c -o mergeVCF.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c processExons.c -o processExons.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c propmapped.c -o propmapped.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c qualityScores.c -o qualityScores.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read-repair.c -o read-repair.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readSummary.c -o readSummary.o
readSummary.c: In function 'vote_and_add_count':
readSummary.c:4938:31: warning: 'longest_overlap_score' may be used uninitialized in this function [-Wmaybe-uninitialized]
4938 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0;
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c removeDupReads.c -o removeDupReads.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam2bed.c -o sam2bed.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sambam-file.c -o sambam-file.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c seek-zlib.c -o seek-zlib.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sorted-hashtable.c -o sorted-hashtable.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sublog.c -o sublog.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.12.3\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tx-unique.c -o tx-unique.o
gcc -shared -s -static-libgcc -o Rsubread.dll tmp.def 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 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-Rsubread/00new/Rsubread/libs/x64
** 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
** 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 | 29.14 | 3.50 | 32.74 | |
| buildindex | 10.08 | 1.92 | 12.03 | |
| cellCounts | 0 | 0 | 0 | |
| featureCounts | 0 | 0 | 0 | |
| findCommonVariants | 0 | 0 | 0 | |
| getInBuiltAnnotation | 0.29 | 0.03 | 0.79 | |
| promoterRegions | 2.24 | 0.02 | 2.27 | |
| propmapped | 27.64 | 4.19 | 32.50 | |
| qualityScores | 0.05 | 0.00 | 0.06 | |
| simReads | 0 | 0 | 0 | |
| sublong | 24.23 | 4.62 | 28.52 | |