Wei Shi
| Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/Rsubread |
| git_branch: devel |
| git_last_commit: 3b42665 |
| git_last_commit_date: 2025-01-09 19:38:01 -0500 (Thu, 09 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-11 11:42 -0500 (Sat, 11 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4760 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4443 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4391 |
| 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 1797/2277 | 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 | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | 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: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rsubread.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Rsubread_2.21.1.tar.gz |
| StartedAt: 2025-01-11 04:58:23 -0500 (Sat, 11 Jan 2025) |
| EndedAt: 2025-01-11 05:02:12 -0500 (Sat, 11 Jan 2025) |
| EllapsedTime: 229.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Rsubread.Rcheck |
| Warnings: 1 |
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### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rsubread.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Rsubread_2.21.1.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/Rsubread.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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=]
readSummary.c:870:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'srInt_64' {aka 'long long int'} [-Wformat=]
See 'E:/biocbuild/bbs-3.21-bioc/meat/Rsubread.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* checking installed package size ... INFO
installed size is 36.8Mb
sub-directories of 1Mb or more:
annot 30.9Mb
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 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 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 'E:/biocbuild/bbs-3.21-bioc/R/library/Rsubread/libs/x64/Rsubread.dll':
Found '_exit', possibly from '_exit' (C)
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 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 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 38.49 7.14 46.11
propmapped 38.28 6.52 45.28
sublong 35.56 6.56 41.72
buildindex 12.17 3.35 15.59
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
'E:/biocbuild/bbs-3.21-bioc/meat/Rsubread.Rcheck/00check.log'
for details.
Rsubread.Rcheck/00install.out
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###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Rsubread
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'Rsubread' ...
** using staged installation
@@@@@ The operating system is Windows.
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c HelperFunctions.c -o HelperFunctions.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LRMbase-index.c -o LRMbase-index.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LRMchro-event.c -o LRMchro-event.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LRMfile-io.c -o LRMfile-io.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LRMhashtable.c -o LRMhashtable.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LRMhelper.c -o LRMhelper.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_wrapper.c -o R_wrapper.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RsimReads.c -o RsimReads.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SNPCalling.c -o SNPCalling.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c aligner.c -o aligner.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c atgcContent.c -o atgcContent.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c build-sam-index.c -o build-sam-index.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -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:1622:19: warning: 'search_start' may be used uninitialized [-Wmaybe-uninitialized]
1622 | if(search_start>0xffffff00) return;
| ^
cell-counts.c:1611:30: note: 'search_start' was declared here
1611 | unsigned int search_start, search_end, search_block_id;
| ^~~~~~~~~~~~
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c core-bigtable.c -o core-bigtable.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c core-indel.c -o core-indel.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c core-interface-aligner.c -o core-interface-aligner.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c core-junction.c -o core-junction.o
core-junction.c: In function 'find_donor_receptor':
core-junction.c:2099:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0)
| ^~
core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){
| ^~
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c core.c -o core.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c detection-calls.c -o detection-calls.o
detection-calls.c: In function 'DTCwrite_annotations':
detection-calls.c:155:9: warning: dangling pointer 'gc_2int' to an unnamed temporary may be used [-Wdangling-pointer=]
155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
detection-calls.c:154:48: note: unnamed temporary defined here
154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0};
| ^
detection-calls.c:155:109: warning: dangling pointer 'gc_2int' to an unnamed temporary may be used [-Wdangling-pointer=]
155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0);
| ^
detection-calls.c:154:48: note: unnamed temporary defined here
154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0};
| ^
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c detectionCall.c -o detectionCall.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c exon-algorithms.c -o exon-algorithms.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c exon-align-indel.c -o exon-align-indel.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c exon-align.c -o exon-align.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c flattenAnnotations.c -o flattenAnnotations.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fullscan.c -o fullscan.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fusion-align.c -o fusion-align.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gen_rand_reads.c -o gen_rand_reads.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gene-algorithms.c -o gene-algorithms.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gene-value-index.c -o gene-value-index.o
gene-value-index.c: In function 'is_offset_in_chro':
gene-value-index.c:85:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
85 | if( pos < chros -> padding || pos >= ( chros->read_offsets[n] - chros->read_offsets[n-1] - chros -> padding ))
| ^~
In file included from gene-value-index.h:24,
from gene-value-index.c:25:
subread.h:153:24: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
153 | #define SUBREADprintf msgqu_printf
| ^~~~~~~~~~~~
gene-value-index.c:87:41: note: in expansion of macro 'SUBREADprintf'
87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos);
| ^~~~~~~~~~~~~
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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
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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c index-builder.c -o index-builder.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c input-blc.c -o input-blc.o
input-blc.c: In function 'iCache_continuous_read_lanes':
input-blc.c:580:59: warning: unused variable 'npos' [-Wunused-variable]
580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET);
| ^~~~
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c input-files.c -o input-files.o
input-files.c: In function 'reduce_SAM_to_BAM':
input-files.c:3244:13: warning: unused variable 'seq_len' [-Wunused-variable]
3244 | int seq_len = qual - seq - 1;
| ^~~~~~~
input-files.c: In function 'SAM_pairer_fix_format':
input-files.c:4863:50: warning: variable 'readname' set but not used [-Wunused-but-set-variable]
4863 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256];
| ^~~~~~~~
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c interval_merge.c -o interval_merge.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c long-hashtable.c -o long-hashtable.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c longread-mapping.c -o longread-mapping.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mergeVCF.c -o mergeVCF.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c processExons.c -o processExons.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c propmapped.c -o propmapped.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c qualityScores.c -o qualityScores.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read-repair.c -o read-repair.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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
readSummary.c: In function 'sort_junc_feature':
readSummary.c:870:49: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'srInt_64' {aka 'long long int'} [-Wformat=]
870 | fprintf(stderr,"MERGED GeneBodyTree = %ld\n", global_context -> junction_GenebodyTree_table -> numOfElements);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long int srInt_64 {aka long long int}
| %lld
readSummary.c: In function 'vote_and_add_count':
readSummary.c:3840:58: warning: variable 'assignment_target_number' set but not used [-Wunused-but-set-variable]
3840 | srInt_64 assignment_target_number = tmp_voter_id;
| ^~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function 'fc_thread_merge_results':
readSummary.c:3910:32: warning: unused variable 'sample_i' [-Wunused-variable]
3910 | int xk1, xk2, ret = 0, sample_i;
| ^~~~~~~~
readSummary.c: In function 'determine_jcount_gene_transcript_report':
readSummary.c:5460:29: warning: unused variable 'this_exons' [-Wunused-variable]
5460 | int this_exons=0;
| ^~~~~~~~~~
readSummary.c:5469:29: warning: unused variable 'this_exons' [-Wunused-variable]
5469 | int this_exons=0;
| ^~~~~~~~~~
readSummary.c: In function 'fc_write_final_junctions':
readSummary.c:5591:21: warning: unused variable 'unique_junctions' [-Wunused-variable]
5591 | int unique_junctions = 0;
| ^~~~~~~~~~~~~~~~
readSummary.c:5575:20: warning: unused variable 'ky_i2' [-Wunused-variable]
5575 | int ky_i1, ky_i2;
| ^~~~~
readSummary.c:5575:13: warning: unused variable 'ky_i1' [-Wunused-variable]
5575 | int ky_i1, ky_i2;
| ^~~~~
readSummary.c:5573:81: warning: unused variable 'gene_name_tail' [-Wunused-variable]
5573 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
| ^~~~~~~~~~~~~~
readSummary.c: In function 'readSummary':
readSummary.c:5787:52: warning: variable 'scrna_total_BAM_no' set but not used [-Wunused-but-set-variable]
5787 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no;
| ^~~~~~~~~~~~~~~~~~
readSummary.c: In function 'register_junc_feature.part.0':
readSummary.c:876:35: warning: array subscript 'fc_junction_exon_in_transcript_t[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
876 | new_item -> transcript_id = HashTableGetKey(global_context -> junction_transcript_table, transcript_id);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:875:55: note: object of size 8 allocated by 'calloc'
875 | fc_junction_exon_in_transcript_t * new_item = calloc(sizeof(sizeof(fc_junction_exon_in_transcript_t)),1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:878:43: warning: array subscript 'fc_junction_exon_in_transcript_t[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
878 | new_item -> transcript_id = strdup(transcript_id);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:875:55: note: object of size 8 allocated by 'calloc'
875 | fc_junction_exon_in_transcript_t * new_item = calloc(sizeof(sizeof(fc_junction_exon_in_transcript_t)),1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:884:83: warning: array subscript 'fc_junction_exon_in_transcript_t[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
884 | HashTablePut(global_context -> junction_transcript_table, new_item->transcript_id, new_txp);
| ~~~~~~~~^~~~~~~~~~~~~~~
readSummary.c:875:55: note: object of size 8 allocated by 'calloc'
875 | fc_junction_exon_in_transcript_t * new_item = calloc(sizeof(sizeof(fc_junction_exon_in_transcript_t)),1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:890:32: warning: array subscript 'fc_junction_exon_in_transcript_t[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
890 | new_item -> chro_start = start;
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
readSummary.c:875:55: note: object of size 8 allocated by 'calloc'
875 | fc_junction_exon_in_transcript_t * new_item = calloc(sizeof(sizeof(fc_junction_exon_in_transcript_t)),1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:891:31: warning: array subscript 'fc_junction_exon_in_transcript_t[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
891 | new_item -> chro_stop = stop;
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~
readSummary.c:875:55: note: object of size 8 allocated by 'calloc'
875 | fc_junction_exon_in_transcript_t * new_item = calloc(sizeof(sizeof(fc_junction_exon_in_transcript_t)),1);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function 'vote_and_add_count':
readSummary.c:3773:66: warning: 'longest_overlap_score' may be used uninitialized [-Wmaybe-uninitialized]
3773 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0;
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:3542:51: note: 'longest_overlap_score' was declared here
3542 | int scoring_count = 0, score_x1, longest_overlap_score;
| ^~~~~~~~~~~~~~~~~~~~~
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c removeDupReads.c -o removeDupReads.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sam2bed.c -o sam2bed.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sambam-file.c -o sambam-file.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c seek-zlib.c -o seek-zlib.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sorted-hashtable.c -o sorted-hashtable.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sublog.c -o sublog.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-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 | 38.49 | 7.14 | 46.11 | |
| buildindex | 12.17 | 3.35 | 15.59 | |
| cellCounts | 0 | 0 | 0 | |
| featureCounts | 0 | 0 | 0 | |
| findCommonVariants | 0 | 0 | 0 | |
| getInBuiltAnnotation | 0.39 | 0.14 | 0.79 | |
| promoterRegions | 3.26 | 0.08 | 3.58 | |
| propmapped | 38.28 | 6.52 | 45.28 | |
| qualityScores | 0.08 | 0.00 | 0.09 | |
| simReads | 0 | 0 | 0 | |
| sublong | 35.56 | 6.56 | 41.72 | |