Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:53 -0400 (Fri, 15 Oct 2021).

CHECK results for ShortRead on nebbiolo1

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? here 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 1753/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ShortRead 1.50.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/ShortRead
git_branch: RELEASE_3_13
git_last_commit: 31dea4d
git_last_commit_date: 2021-05-19 11:40:52 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ShortRead
Version: 1.50.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ShortRead.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ShortRead_1.50.0.tar.gz
StartedAt: 2021-10-14 11:36:37 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:40:16 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 218.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ShortRead.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ShortRead.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ShortRead_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ShortRead.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.50.0’
* 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-3.13-bioc/meat/ShortRead.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R         1.8Mb
    extdata   3.3Mb
* 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 6.009  0.219    6.24
* 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-3.13-bioc/meat/ShortRead.Rcheck/00check.log’
for details.



Installation output

ShortRead.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ShortRead
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.13-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-3.13-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-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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Welcome to Bioconductor

    Vignettes contain introductory material; view with
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    'citation("Biobase")', and for packages 'citation("pkgname")'.


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RUNIT TEST PROTOCOL -- Thu Oct 14 11:40:09 2021 
*********************************************** 
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: closing unused connection 6 (/home/biocbuild/bbs-3.13-bioc/R/library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt) 
2: closing unused connection 5 (/home/biocbuild/bbs-3.13-bioc/R/library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt) 
> 
> proc.time()
   user  system elapsed 
 20.529   1.987  21.903 

Example timings

ShortRead.Rcheck/ShortRead-Ex.timings

nameusersystemelapsed
AlignedRead-class0.2540.0650.319
BowtieQA-class0.0010.0000.001
ExperimentPath-class000
FastqQA-class0.0000.0010.001
Intensity-class0.1220.0210.147
MAQMapQA-class0.0000.0000.001
QA-class0.0000.0010.001
QualityScore-class0.0100.0020.012
QualityScore0.0340.0000.034
RochePath-class0.0010.0000.001
RocheSet-class0.0010.0000.001
RtaIntensity-class0.0350.0030.039
RtaIntensity0.0230.0040.027
SRFilter-class0.0010.0000.000
SRFilterResult-class0.0380.0070.045
SRSet-class0.0010.0000.001
SRUtil-class0.0040.0000.005
Sampler-class1.0890.0081.098
ShortRead-class0.0390.0040.043
ShortReadQ-class0.1990.0160.214
Snapshot-class6.0090.2196.240
SnapshotFunction-class0.0010.0000.001
SolexaExportQA-class0.0010.0000.001
SolexaIntensity-class0.1030.0040.108
SolexaPath-class0.0610.0030.065
SolexaSet-class0.0450.0050.050
SpTrellis-class0.3020.0070.310
accessors0.0020.0000.002
alphabetByCycle0.0170.0110.028
clean0.0000.0000.001
countLines0.1060.0080.119
dotQA-class0.0010.0000.001
dustyScore0.2570.0000.257
filterFastq1.2180.0121.230
polyn0.0010.0000.001
qa0.4340.0080.442
qa22.9020.0492.953
readAligned0.1680.0110.179
readBaseQuality2.2830.0242.301
readFasta0.0710.0040.076
readFastq0.0930.0040.097
readIntensities0.0440.0040.049
readPrb0.0260.0080.034
readQseq0.0090.0000.008
readXStringColumns0.0400.0040.043
renew0.0240.0080.033
report0.0000.0030.004
spViewPerFeature2.5930.1042.697
srFilter0.2580.0080.267
srdistance0.1720.1220.263
srduplicated0.0940.0980.061
tables0.1100.0120.122
trimTails0.0290.0000.029