| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:41:16 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 1943/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ShortRead 1.60.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: ShortRead |
| Version: 1.60.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ShortRead.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ShortRead_1.60.0.tar.gz |
| StartedAt: 2023-11-02 14:21:16 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 14:26:47 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 331.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ShortRead.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ShortRead.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ShortRead_1.60.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ShortRead.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ShortRead/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ShortRead’ version ‘1.60.0’
* 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 ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* 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 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 ... 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.3.1/site-library/ShortRead/libs/ShortRead.so’:
Found ‘sprintf’, 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 8.867 0.104 9.011
qa2 5.322 0.163 5.507
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘ShortRead_unit_tests.R’
ERROR
Running the tests in ‘tests/ShortRead_unit_tests.R’ failed.
Last 13 lines of output:
FALSE
FAILURE in test_readPrb_input: Error in checkIdentical(36L, unique(width(obj))) : FALSE
Test files with failing tests
test_readPrb.R
test_readPrb_consistent
test_readPrb_input
Error in BiocGenerics:::testPackage("ShortRead") :
unit tests failed for package ShortRead
Execution halted
* 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 ERROR, 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/ShortRead.Rcheck/00check.log’
for details.
ShortRead.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL ShortRead ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/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 (GCC) 10.3.1’ using C++ compiler: ‘g++ (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c alphabet.c -o alphabet.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c count.c -o count.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c io.c -o io.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c io_bowtie.c -o io_bowtie.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-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 g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c sampler.c -o sampler.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c trim.c -o trim.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c util.c -o util.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c xsnap.c -o xsnap.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/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)
ShortRead.Rcheck/tests/ShortRead_unit_tests.Rout.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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> 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, setdiff, sort, 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
Timing stopped at: 0.073 0.157 0.178
Error in checkIdentical(exp, as(readPrb(sp, ".*prb.txt", as = "FastqEncoding"), :
FALSE
Timing stopped at: 0.043 0.152 0.116
Error in checkIdentical(36L, unique(width(obj))) : FALSE
RUNIT TEST PROTOCOL -- Thu Nov 2 14:26:41 2023
***********************************************
Number of test functions: 106
Number of errors: 0
Number of failures: 2
1 Test Suite :
ShortRead RUnit Tests - 106 test functions, 0 errors, 2 failures
FAILURE in test_readPrb_consistent: Error in checkIdentical(exp, as(readPrb(sp, ".*prb.txt", as = "FastqEncoding"), :
FALSE
FAILURE in test_readPrb_input: Error in checkIdentical(36L, unique(width(obj))) : FALSE
Test files with failing tests
test_readPrb.R
test_readPrb_consistent
test_readPrb_input
Error in BiocGenerics:::testPackage("ShortRead") :
unit tests failed for package ShortRead
Execution halted
ShortRead.Rcheck/ShortRead-Ex.timings
| name | user | system | elapsed | |
| AlignedRead-class | 0.352 | 0.044 | 0.398 | |
| BowtieQA-class | 0.001 | 0.000 | 0.001 | |
| ExperimentPath-class | 0.000 | 0.001 | 0.001 | |
| FastqQA-class | 0 | 0 | 0 | |
| Intensity-class | 0.168 | 0.029 | 0.203 | |
| MAQMapQA-class | 0.001 | 0.000 | 0.001 | |
| QA-class | 0.000 | 0.001 | 0.001 | |
| QualityScore-class | 0.009 | 0.002 | 0.012 | |
| QualityScore | 0.007 | 0.000 | 0.006 | |
| RochePath-class | 0.001 | 0.000 | 0.001 | |
| RocheSet-class | 0.000 | 0.000 | 0.001 | |
| RtaIntensity-class | 0.058 | 0.008 | 0.066 | |
| RtaIntensity | 0.037 | 0.000 | 0.037 | |
| SRFilter-class | 0 | 0 | 0 | |
| SRFilterResult-class | 0.049 | 0.015 | 0.063 | |
| SRSet-class | 0.001 | 0.000 | 0.000 | |
| SRUtil-class | 0.001 | 0.003 | 0.005 | |
| Sampler-class | 1.266 | 0.016 | 1.286 | |
| ShortRead-class | 0.066 | 0.000 | 0.066 | |
| ShortReadQ-class | 0.304 | 0.004 | 0.309 | |
| Snapshot-class | 8.867 | 0.104 | 9.011 | |
| SnapshotFunction-class | 0.001 | 0.000 | 0.000 | |
| SolexaExportQA-class | 0.000 | 0.000 | 0.001 | |
| SolexaIntensity-class | 0.113 | 0.004 | 0.118 | |
| SolexaPath-class | 0.091 | 0.000 | 0.092 | |
| SolexaSet-class | 0.075 | 0.000 | 0.074 | |
| SpTrellis-class | 0.409 | 0.036 | 0.446 | |
| accessors | 0.000 | 0.002 | 0.002 | |
| alphabetByCycle | 0.028 | 0.001 | 0.030 | |
| clean | 0.001 | 0.000 | 0.001 | |
| countLines | 0.074 | 0.016 | 0.103 | |
| dotQA-class | 0.001 | 0.000 | 0.001 | |
| dustyScore | 0.068 | 0.000 | 0.067 | |
| filterFastq | 1.193 | 0.000 | 1.196 | |
| polyn | 0.001 | 0.000 | 0.001 | |
| qa | 0.608 | 0.004 | 0.614 | |
| qa2 | 5.322 | 0.163 | 5.507 | |
| readAligned | 0.222 | 0.001 | 0.222 | |
| readBaseQuality | 4.432 | 0.055 | 4.515 | |
| readFasta | 0.102 | 0.091 | 0.117 | |
| readFastq | 0.136 | 0.021 | 0.157 | |
| readIntensities | 0.073 | 0.015 | 0.088 | |
| readPrb | 0.044 | 0.036 | 0.101 | |
| readQseq | 0.011 | 0.008 | 0.019 | |
| readXStringColumns | 0.082 | 0.091 | 0.090 | |
| renew | 0.051 | 0.030 | 0.081 | |
| report | 0.005 | 0.001 | 0.007 | |
| spViewPerFeature | 3.069 | 0.471 | 3.548 | |
| srFilter | 0.333 | 0.072 | 0.407 | |
| srdistance | 0.139 | 0.355 | 0.412 | |
| srduplicated | 0.151 | 0.182 | 0.080 | |
| tables | 0.134 | 0.019 | 0.154 | |
| trimTails | 0.036 | 0.004 | 0.040 | |