Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1809/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rsubread 2.20.0 (landing page) Wei Shi
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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: 2.20.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rsubread.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Rsubread_2.20.0.tar.gz |
StartedAt: 2024-12-20 05:29:42 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:33:39 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 237.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Rsubread.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rsubread.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Rsubread_2.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Rsubread.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * 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 '2.20.0' * 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 * used C compiler: 'gcc.exe (GCC) 13.3.0' * checking installed package size ... NOTE installed size is 36.7Mb 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 'F:/biocbuild/bbs-3.20-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 40.55 7.14 47.78 propmapped 39.03 7.04 46.53 sublong 35.89 6.30 41.69 buildindex 13.53 3.89 17.44 * 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: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/Rsubread.Rcheck/00check.log' for details.
Rsubread.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Rsubread ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c HelperFunctions.c -o HelperFunctions.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LRMbase-index.c -o LRMbase-index.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LRMchro-event.c -o LRMchro-event.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LRMfile-io.c -o LRMfile-io.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LRMhashtable.c -o LRMhashtable.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LRMhelper.c -o LRMhelper.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LRMseek-zlib.c -o LRMseek-zlib.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_wrapper.c -o R_wrapper.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RsimReads.c -o RsimReads.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SNPCalling.c -o SNPCalling.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c aligner.c -o aligner.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c atgcContent.c -o atgcContent.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c build-sam-index.c -o build-sam-index.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c core-bigtable.c -o core-bigtable.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c core-indel.c -o core-indel.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c core-interface-aligner.c -o core-interface-aligner.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c core-interface-subjunc.c -o core-interface-subjunc.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c core.c -o core.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c detectionCall.c -o detectionCall.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c detectionCallAnnotation.c -o detectionCallAnnotation.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c exon-algorithms.c -o exon-algorithms.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c exon-align-indel.c -o exon-align-indel.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c exon-align.c -o exon-align.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c flattenAnnotations.c -o flattenAnnotations.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fullscan.c -o fullscan.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fusion-align.c -o fusion-align.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gen_rand_reads.c -o gen_rand_reads.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gene-algorithms.c -o gene-algorithms.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hashtable.c -o hashtable.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c index-builder.c -o index-builder.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -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:4834:50: warning: variable 'readname' set but not used [-Wunused-but-set-variable] 4834 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256]; | ^~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c interval_merge.c -o interval_merge.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c long-hashtable.c -o long-hashtable.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c longread-mapping.c -o longread-mapping.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mergeVCF.c -o mergeVCF.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c processExons.c -o processExons.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c propmapped.c -o propmapped.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c qualityScores.c -o qualityScores.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read-repair.c -o read-repair.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readSummary.c -o readSummary.o readSummary.c: In function 'vote_and_add_count': readSummary.c:3819:58: warning: variable 'assignment_target_number' set but not used [-Wunused-but-set-variable] 3819 | srInt_64 assignment_target_number = tmp_voter_id; | ^~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c: In function 'fc_thread_merge_results': readSummary.c:3889:32: warning: unused variable 'sample_i' [-Wunused-variable] 3889 | int xk1, xk2, ret = 0, sample_i; | ^~~~~~~~ readSummary.c: In function 'readSummary': readSummary.c:5645:52: warning: variable 'scrna_total_BAM_no' set but not used [-Wunused-but-set-variable] 5645 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no; | ^~~~~~~~~~~~~~~~~~ readSummary.c: In function 'vote_and_add_count': readSummary.c:3752:66: warning: 'longest_overlap_score' may be used uninitialized [-Wmaybe-uninitialized] 3752 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:3521:51: note: 'longest_overlap_score' was declared here 3521 | int scoring_count = 0, score_x1, longest_overlap_score; | ^~~~~~~~~~~~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c removeDupReads.c -o removeDupReads.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sam2bed.c -o sam2bed.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sambam-file.c -o sambam-file.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c seek-zlib.c -o seek-zlib.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sorted-hashtable.c -o sorted-hashtable.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sublog.c -o sublog.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.20.0\"" -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 -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-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 | 40.55 | 7.14 | 47.78 | |
buildindex | 13.53 | 3.89 | 17.44 | |
cellCounts | 0 | 0 | 0 | |
featureCounts | 0 | 0 | 0 | |
findCommonVariants | 0 | 0 | 0 | |
getInBuiltAnnotation | 0.47 | 0.05 | 0.66 | |
promoterRegions | 2.39 | 0.03 | 2.58 | |
propmapped | 39.03 | 7.04 | 46.53 | |
qualityScores | 0.09 | 0.00 | 0.13 | |
simReads | 0 | 0 | 0 | |
sublong | 35.89 | 6.30 | 41.69 | |