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 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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 1948/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ShortRead 1.64.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/ShortRead
git_branch: RELEASE_3_20
git_last_commit: 88fd3ab
git_last_commit_date: 2024-10-29 09:29:09 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for ShortRead on nebbiolo2

To the developers/maintainers of the ShortRead package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ShortRead.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: ShortRead
Version: 1.64.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ShortRead.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ShortRead_1.64.0.tar.gz
StartedAt: 2024-12-20 05:28:27 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 05:32:40 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 253.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ShortRead.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ShortRead.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ShortRead_1.64.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ShortRead.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ShortRead/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ShortRead’ version ‘1.64.0’
* 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 ‘ShortRead’ can be installed ... WARNING
Found the following significant warnings:
  io.c:227:38: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘const char *’ [-Wformat=]
  io.c:658:49: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
  io.c:676:48: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
  readBfaToc.cc:35:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  readBfaToc.cc:36:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  readBfaToc.cc:37:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/ShortRead.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... NOTE
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R         2.2Mb
    extdata   4.0Mb
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::V_recycle’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotCycleBaseCall: no visible binding for global variable ‘Base’
flag,QAReadQuality: no visible binding for global variable ‘Score’
flag,QAReadQuality: no visible binding for global variable ‘Id’
flag,QAReadQuality: no visible binding for global variable ‘Density’
report,QAFrequentSequence: no visible binding for global variable
  ‘TopCount’
report,QAFrequentSequence: no visible binding for global variable ‘Id’
report,QANucleotideByCycle: no visible binding for global variable
  ‘Base’
report,QANucleotideUse: no visible binding for global variable
  ‘Nucleotide’
report,QAQualityUse: no visible binding for global variable ‘Count’
report,QAQualityUse: no visible binding for global variable ‘Id’
report,QAQualityUse: no visible binding for global variable ‘Quality’
report,QAReadQuality: no visible binding for global variable ‘Id’
report,QASequenceUse: no visible binding for global variable
  ‘Occurrences’
report,QASequenceUse: no visible binding for global variable ‘Id’
report,QASequenceUse: no visible binding for global variable ‘Reads’
Undefined global functions or variables:
  Base Count Density Id Nucleotide Occurrences Quality Reads Score
  TopCount
* checking Rd files ... NOTE
checkRd: (-1) deprecated.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deprecated.Rd:23-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... NOTE
Invalid package aliases in Rd file 'ShortRead-package.Rd':
  ‘ShortReadBase-package’
* 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/ShortRead/libs/ShortRead.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)

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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
Snapshot-class 4.856  0.168   5.035
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘ShortRead_unit_tests.R’
 OK
* 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 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/ShortRead.Rcheck/00check.log’
for details.


Installation output

ShortRead.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘ShortRead’ ...
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 8
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c alphabet.c -o alphabet.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c count.c -o count.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c io.c -o io.o
io.c: In function ‘read_prb_as_character’:
io.c:227:38: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘const char *’ [-Wformat=]
  227 |         error("could not read file '%f'", translateChar(STRING_ELT(fname, 0)));
      |                                     ~^
      |                                      |
      |                                      double
      |                                     %s
io.c: In function ‘_read_solexa_export_file’:
io.c:658:49: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
  658 |                 error("invalid 'strand' field '%s', %s:%d",
      |                                                ~^
      |                                                 |
      |                                                 char *
      |                                                %d
  659 |                       *elt[13], fname, lineno);
      |                       ~~~~~~~~                   
      |                       |
      |                       int
io.c:676:48: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=]
  676 |             error("invalid 'filtering' field '%s', %s:%d",
      |                                               ~^
      |                                                |
      |                                                char *
      |                                               %d
  677 |                   *elt[21], fname, lineno);
      |                   ~~~~~~~~                      
      |                   |
      |                   int
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c io_bowtie.c -o io_bowtie.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c io_soap.c -o io_soap.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic  -g -O2  -Wall  -c readBfaToc.cc -o readBfaToc.o
readBfaToc.cc: In function ‘SEXPREC* readBfaToc(SEXP)’:
readBfaToc.cc:35:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   35 |       (void) fread( seq_name, sizeof(char), name_len, fp );
      |              ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readBfaToc.cc:36:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   36 |       (void) fread( &seq_ori_len, sizeof(int), 1, fp );
      |              ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readBfaToc.cc:37:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   37 |       (void) fread( &seq_len, sizeof(int), 1, fp );
      |              ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic  -g -O2  -Wall  -c read_maq_map.cc -o read_maq_map.o
In file included from read_maq_map.cc:13:
maqmap_m.h: In function ‘maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 128]’:
maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free]
  102 |             Rf_error("MAQ format '%d' not supported", mm->format);
      |             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 128]’,
    inlined from ‘void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 128]’ at maqmap_m.h:74:35,
    inlined from ‘maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 128]’ at maqmap_m.h:101:30:
maqmap_m.h:84:14: note: call to ‘void free(void*)’ here
   84 |     std::free(mm);
      |     ~~~~~~~~~^~~~
maqmap_m.h: In function ‘maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 64]’:
maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free]
  102 |             Rf_error("MAQ format '%d' not supported", mm->format);
      |             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 64]’,
    inlined from ‘void maq_delete_maqmap(maqmap_T<max_readlen>*) [with int max_readlen = 64]’ at maqmap_m.h:74:35,
    inlined from ‘maqmap_T<max_readlen>* maqmap_read_header(gzFile) [with int max_readlen = 64]’ at maqmap_m.h:101:30:
maqmap_m.h:84:14: note: call to ‘void free(void*)’ here
   84 |     std::free(mm);
      |     ~~~~~~~~~^~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c sampler.c -o sampler.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c trim.c -o trim.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c util.c -o util.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Biostrings/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhtslib/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c xsnap.c -o xsnap.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-ShortRead/00new/ShortRead/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 (ShortRead)

Tests output

ShortRead.Rcheck/tests/ShortRead_unit_tests.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("ShortRead")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians



RUNIT TEST PROTOCOL -- Fri Dec 20 05:32:17 2024 
*********************************************** 
Number of test functions: 106 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ShortRead RUnit Tests - 106 test functions, 0 errors, 0 failures
Number of test functions: 106 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 17.345   1.643  18.372 

Example timings

ShortRead.Rcheck/ShortRead-Ex.timings

nameusersystemelapsed
AlignedRead-class0.2360.0570.294
BowtieQA-class0.0010.0000.001
ExperimentPath-class0.0010.0000.000
FastqQA-class0.0000.0010.000
Intensity-class0.0980.0300.130
MAQMapQA-class000
QA-class0.0010.0000.001
QualityScore-class0.0050.0020.007
QualityScore0.0020.0030.004
RochePath-class000
RocheSet-class0.0010.0000.000
RtaIntensity-class0.0350.0100.045
RtaIntensity0.0260.0020.027
SRFilter-class000
SRFilterResult-class0.0380.0050.044
SRSet-class0.0000.0000.001
SRUtil-class0.0020.0010.003
Sampler-class0.9160.0100.926
ShortRead-class0.0400.0000.039
ShortReadQ-class0.1910.0030.195
Snapshot-class4.8560.1685.035
SnapshotFunction-class0.0010.0000.000
SolexaExportQA-class0.0010.0000.000
SolexaIntensity-class0.0710.0040.076
SolexaPath-class0.0600.0010.060
SolexaSet-class0.0500.0000.049
SpTrellis-class0.3300.0030.333
accessors0.0010.0000.002
alphabetByCycle0.0190.0000.019
clean0.0010.0000.000
countLines0.1010.0020.106
dotQA-class000
dustyScore0.2190.0000.219
filterFastq0.9070.0010.909
polyn0.0010.0000.001
qa0.4100.0140.424
qa22.7830.1452.919
readAligned0.1450.0050.150
readBaseQuality3.6210.1943.832
readFasta0.0780.0490.077
readFastq0.0930.0050.098
readIntensities0.0370.0080.045
readPrb0.0240.0370.078
readQseq0.0070.0030.011
readXStringColumns0.0560.0460.050
renew0.0290.0050.034
report0.0020.0000.003
spViewPerFeature2.3060.1842.491
srFilter0.2250.0120.238
srdistance0.1390.3210.333
srduplicated0.0710.0630.047
tables0.1090.0140.123
trimTails0.0190.0070.026