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This page was generated on 2024-06-13 12:18 -0400 (Thu, 13 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4344
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 1774/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 2.19.0  (landing page)
Wei Shi , Yang Liao and Gordon K Smyth
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/Rsubread
git_branch: devel
git_last_commit: ff20753
git_last_commit_date: 2024-04-30 10:23:58 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for Rsubread on nebbiolo2

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.

raw results


Summary

Package: Rsubread
Version: 2.19.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Rsubread_2.19.0.tar.gz
StartedAt: 2024-06-13 03:04:31 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 03:14:18 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 586.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Rsubread.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Rsubread_2.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Rsubread.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* this is package ‘Rsubread’ version ‘2.19.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Rsubread’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is 39.2Mb
  sub-directories of 1Mb or more:
    annot  30.9Mb
    libs    3.4Mb
    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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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 27.139 13.818  42.806
align      27.286 13.583  40.899
sublong    20.138  5.936  25.933
buildindex  7.461  2.586  11.953
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Rsubread.Rcheck/00check.log’
for details.


Installation output

Rsubread.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Rsubread
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘Rsubread’ ...
** using staged installation
@@@@@ The operating system is Linux.
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c HelperFunctions.c -o HelperFunctions.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c LRMbase-index.c -o LRMbase-index.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c LRMchro-event.c -o LRMchro-event.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c LRMfile-io.c -o LRMfile-io.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c LRMhashtable.c -o LRMhashtable.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c LRMhelper.c -o LRMhelper.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c R_wrapper.c -o R_wrapper.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c RsimReads.c -o RsimReads.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c SNPCalling.c -o SNPCalling.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c aligner.c -o aligner.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c atgcContent.c -o atgcContent.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c build-sam-index.c -o build-sam-index.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c cell-counts.c -o cell-counts.o
cell-counts.c: In function ‘cellCounts_find_hits_for_mapped_section’:
cell-counts.c:1621:19: warning: ‘search_start’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1621 |                 if(search_start>0xffffff00) return;
      |                   ^
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c core-bigtable.c -o core-bigtable.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c core-indel.c -o core-indel.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c core-interface-aligner.c -o core-interface-aligner.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c core.c -o core.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c detection-calls.c -o detection-calls.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c detectionCall.c -o detectionCall.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c exon-algorithms.c -o exon-algorithms.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c exon-align-indel.c -o exon-align-indel.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c exon-align.c -o exon-align.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c flattenAnnotations.c -o flattenAnnotations.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c fullscan.c -o fullscan.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c fusion-align.c -o fusion-align.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c gen_rand_reads.c -o gen_rand_reads.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c gene-algorithms.c -o gene-algorithms.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c hashtable.c -o hashtable.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c index-builder.c -o index-builder.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c input-files.c -o input-files.o
input-files.c: In function ‘reduce_SAM_to_BAM’:
input-files.c:3242:13: warning: unused variable ‘seq_len’ [-Wunused-variable]
 3242 |         int seq_len = qual - seq - 1;
      |             ^~~~~~~
input-files.c: In function ‘SAM_pairer_fix_format’:
input-files.c:4832:50: warning: variable ‘readname’ set but not used [-Wunused-but-set-variable]
 4832 |         char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256];
      |                                                  ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c interval_merge.c -o interval_merge.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c long-hashtable.c -o long-hashtable.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c longread-mapping.c -o longread-mapping.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c mergeVCF.c -o mergeVCF.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c processExons.c -o processExons.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c propmapped.c -o propmapped.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c qualityScores.c -o qualityScores.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c read-repair.c -o read-repair.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c readSummary.c -o readSummary.o
readSummary.c: In function ‘vote_and_add_count’:
readSummary.c:3804:58: warning: variable ‘assignment_target_number’ set but not used [-Wunused-but-set-variable]
 3804 |                                                 srInt_64 assignment_target_number = tmp_voter_id;
      |                                                          ^~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function ‘fc_thread_merge_results’:
readSummary.c:3874:32: warning: unused variable ‘sample_i’ [-Wunused-variable]
 3874 |         int xk1, xk2, ret = 0, sample_i;
      |                                ^~~~~~~~
readSummary.c: In function ‘readSummary’:
readSummary.c:5635:52: warning: variable ‘scrna_total_BAM_no’ set but not used [-Wunused-but-set-variable]
 5635 |         int  isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no;
      |                                                    ^~~~~~~~~~~~~~~~~~
readSummary.c: In function ‘vote_and_add_count’:
readSummary.c:3737:66: warning: ‘longest_overlap_score’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 3737 |                                         if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0;
      |                                            ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c removeDupReads.c -o removeDupReads.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c sam2bed.c -o sam2bed.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c sambam-file.c -o sambam-file.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c seek-zlib.c -o seek-zlib.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c sorted-hashtable.c -o sorted-hashtable.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c sublog.c -o sublog.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.19.0\""  -fpic  -g -O2  -Wall -c tx-unique.c -o tx-unique.o
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o Rsubread.so HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o cell-counts.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-Rsubread/00new/Rsubread/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rsubread)

Tests output


Example timings

Rsubread.Rcheck/Rsubread-Ex.timings

nameusersystemelapsed
align27.28613.58340.899
buildindex 7.461 2.58611.953
cellCounts000
featureCounts000
findCommonVariants000
getInBuiltAnnotation0.3030.0440.347
promoterRegions1.6730.0041.678
propmapped27.13913.81842.806
qualityScores0.0590.0150.074
simReads000
sublong20.138 5.93625.933