Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:05:52 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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

CHECK results for ShortRead on nebbiolo2


To the developers/maintainers of the ShortRead package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1811/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ShortRead 1.55.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/ShortRead
git_branch: master
git_last_commit: cca7724
git_last_commit_date: 2022-04-26 11:01:12 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ShortRead
Version: 1.55.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:ShortRead.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings ShortRead_1.55.0.tar.gz
StartedAt: 2022-06-23 21:50:36 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 21:54:22 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 226.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ShortRead.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:ShortRead.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings ShortRead_1.55.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/ShortRead.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ShortRead/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ShortRead’ version ‘1.55.0’
* 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:
  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]
See ‘/home/biocbuild/bbs-3.16-bioc/meat/ShortRead.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  7.9Mb
  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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
Snapshot-class 6.21  0.295   6.515
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/ShortRead.Rcheck/00check.log’
for details.



Installation output

ShortRead.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL ShortRead
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/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
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/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-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c alphabet.c -o alphabet.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c count.c -o count.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c io.c -o io.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c io_bowtie.c -o io_bowtie.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c io_soap.c -o io_soap.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/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++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/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
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c sampler.c -o sampler.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c trim.c -o trim.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c util.c -o util.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/zlibbioc/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c xsnap.c -o xsnap.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-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-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/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 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
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Welcome to Bioconductor

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


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RUNIT TEST PROTOCOL -- Thu Jun 23 21:54:15 2022 
*********************************************** 
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 
Warning messages:
1: In for (i in seq_len(n)) { :
  closing unused connection 6 (/home/biocbuild/bbs-3.16-bioc/R/library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
2: In for (i in seq_len(n)) { :
  closing unused connection 5 (/home/biocbuild/bbs-3.16-bioc/R/library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
> 
> proc.time()
   user  system elapsed 
 19.966   2.208  21.206 

Example timings

ShortRead.Rcheck/ShortRead-Ex.timings

nameusersystemelapsed
AlignedRead-class0.3010.0040.306
BowtieQA-class0.0010.0000.001
ExperimentPath-class0.0000.0000.001
FastqQA-class0.0000.0000.001
Intensity-class0.1300.0000.132
MAQMapQA-class000
QA-class000
QualityScore-class0.0070.0000.007
QualityScore0.0050.0000.005
RochePath-class0.0010.0000.001
RocheSet-class0.0010.0000.001
RtaIntensity-class0.0480.0000.048
RtaIntensity0.0220.0030.026
SRFilter-class000
SRFilterResult-class0.0420.0010.041
SRSet-class0.0010.0000.000
SRUtil-class0.0030.0000.003
Sampler-class0.9870.0080.997
ShortRead-class0.0440.0000.044
ShortReadQ-class0.3170.0080.325
Snapshot-class6.2100.2956.515
SnapshotFunction-class0.0010.0000.001
SolexaExportQA-class0.0010.0000.001
SolexaIntensity-class0.0970.0030.101
SolexaPath-class0.0610.0000.062
SolexaSet-class0.0480.0040.053
SpTrellis-class0.3620.0040.367
accessors0.0020.0000.002
alphabetByCycle0.0170.0030.021
clean0.0000.0000.001
countLines0.1070.0070.117
dotQA-class0.0010.0000.001
dustyScore0.1220.0000.122
filterFastq0.9870.1081.095
polyn000
qa0.4410.0040.445
qa23.2220.1193.343
readAligned0.1510.0040.155
readBaseQuality2.0330.1332.217
readFasta0.0910.0550.074
readFastq0.1000.0000.099
readIntensities0.0420.0080.049
readPrb0.0340.0440.134
readQseq0.0480.0550.013
readXStringColumns0.0710.0040.074
renew0.0460.0080.054
report0.0030.0010.003
spViewPerFeature2.5200.1662.687
srFilter0.2310.0120.243
srdistance0.1440.3130.448
srduplicated0.0460.0040.050
tables0.1780.1030.121
trimTails0.0220.0040.025