Wolfgang Kaisers
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/seqTools |
| git_branch: devel |
| git_last_commit: bde189f |
| git_last_commit_date: 2023-10-24 10:40:22 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:37:05 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 1927/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| seqTools 1.37.0 (landing page) Wolfgang Kaisers
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the seqTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seqTools.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. |
| Package: seqTools |
| Version: 1.37.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:seqTools.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings seqTools_1.37.0.tar.gz |
| StartedAt: 2024-03-28 02:40:23 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 02:40:51 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 27.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: seqTools.Rcheck |
| Warnings: 4 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:seqTools.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings seqTools_1.37.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/seqTools.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘seqTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqTools’ version ‘1.37.0’
* 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 ‘seqTools’ can be installed ... WARNING
Found the following significant warnings:
seqTools.c:851:93: warning: format ‘%u’ expects a matching ‘unsigned int’ argument [-Wformat=]
seqTools.c:3296:55: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=]
seqTools.c:3306:73: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=]
See ‘/home/biocbuild/bbs-3.19-bioc/meat/seqTools.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘kmerSvd’
Undocumented S4 methods:
generic 'kmerSvd' and siglist 'Fastqq'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 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-3.19-bioc/R/site-library/seqTools/libs/seqTools.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 ... WARNING
Found the following significant warnings:
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata’, resetting
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’
Running ‘test_seqTools.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: 4 WARNINGs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/seqTools.Rcheck/00check.log’
for details.
seqTools.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL seqTools
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘seqTools’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/zlibbioc/include' -I/usr/local/include -fpic -g -O2 -Wall -c seqTools.c -o seqTools.o
seqTools.c: In function ‘count_genome_Kmers’:
seqTools.c:851:93: warning: format ‘%u’ expects a matching ‘unsigned int’ argument [-Wformat=]
851 | error("[count_genome_Kmers] character mismatch at position %u!");
| ~^
| |
| unsigned int
seqTools.c: In function ‘scale_kmer_matrix’:
seqTools.c:3296:55: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=]
3296 | error("[scale_kmer_matrix] scale[%i]=%i must be >1!", column_index, scale);
| ~^ ~~~~~
| | |
| int double
| %f
seqTools.c:3306:73: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=]
3306 | error("[scale_kmer_matrix] scale[%i] = %i must be >1!", column_index, scale);
| ~^ ~~~~~
| | |
| int double
| %f
gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o seqTools.so seqTools.o -lm -lz -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-seqTools/00new/seqTools/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 (seqTools)
seqTools.Rcheck/tests/test-all.Rout
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
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.
>
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Load prerequisites
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> library(seqTools)
Loading required package: zlibbioc
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Initialize example data
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> basedir<-system.file("extdata",package="seqTools")
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Run tests
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> filename <- "test_seqTools.R"
> basedir <- system.file("extdata", package = "seqTools")
> load(file.path(basedir,"test_res.RData"))
>
>
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## kmerCount.fastqq
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> fq <- fastqq(file.path(basedir, "test_l5_N.fq"), k = 2)
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata/test_l5_N.fq' done.
> if(!identical(kmerCount(fq), kmer_l5_N))
+ stop("[kmerCount.fastqq] Test 1 '", filename, "' FAILED!")
>
> fq<-fastqq(file.path(basedir, "test_l6.fq"), k = 2)
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata/test_l6.fq' done.
> if(!identical(kmerCount(fq), kmer_l6))
+ stop("[kmerCount.fastqq] Test 2 '", filename, "' FAILED!")
>
> fq<-fastqq(file.path(basedir, "test_l6_multi_line.fq"), k = 2)
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata/test_l6_multi_line.fq' done.
> if(!identical(kmerCount(fq), kmer_l6_ml))
+ stop("[kmerCount.fastqq] Test 3 '", filename, "' FAILED!")
>
> fq<-fastqq(file.path(basedir, "test_l10_20_40.fq"),k = 2)
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata/test_l10_20_40.fq' done.
> if(!identical(kmerCount(fq), kmer_l10_20))
+ stop("[kmerCount.fastqq] Test 4 '", filename, "' FAILED!")
>
> fq<-fastqq(file.path(basedir, "test_l10_atcg.fq"), k = 2)
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata/test_l10_atcg.fq' done.
> if(!identical(kmerCount(fq), kmer_l10_atcg))
+ stop("[kmerCount.fastqq] Test 5 '", filename, "' FAILED!")
>
> fq<-fastqq(file.path(basedir, "test_l10_ATCGN.fq"), k = 2)
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.19-bioc/R/site-library/seqTools/extdata/test_l10_ATCGN.fq' done.
> if(!identical(kmerCount(fq), kmer_l10_ATCGN))
+ stop("[kmerCount.fastqq] Test 6 '", filename, "' FAILED!")
>
> # Counting k-mers on linux ('\n') and equal windows ('\r\n')
> # formatted FASTQ file should give equal results
> # fq<-fastqq(file.path(basedir, c("test_l4.fq", "test_win.fq")), k = 2)
> # kc <- kmerCount(fq)
> # if(!all(kc[,1]==kc[,2]))
> # stop("[kmerCount.fastqq] test_l4: kmerCount unequal to test_win.fq")
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## ascii2char, char2ascii
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> if(!identical(ascii2char(97:101, multiple = FALSE), "abcde"))
+ stop("[ascii2char] Test 1 '", filename, "' FAILED!")
>
> if(!identical(ascii2char(97:101, multiple = TRUE), letters[1:5]))
+ stop("[ascii2char] Test 2 '", filename, "' FAILED!")
>
> if(!identical(ascii2char(char2ascii("abcde")), "abcde"))
+ stop("[ascii2char] Test 3 '", filename, "' FAILED!")
>
> if(!identical(char2ascii("abcde"), 97:101))
+ stop("[char2ascii] Test 1 '", filename, "' FAILED!")
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## END OF FILE
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
>
> proc.time()
user system elapsed
0.276 0.025 0.289
seqTools.Rcheck/tests/test_seqTools.Rout
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
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.
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Load prerequisites
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> library(seqTools)
Loading required package: zlibbioc
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Initialize example data
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> basedir<-system.file("extdata",package="seqTools")
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Run tests
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> filename <- "test_seqTools.R"
> basedir <- system.file("extdata", package = "seqTools")
> load(file.path(basedir,"test_res.RData"))
>
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## countDnaKmers
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> if(!identical(countDnaKmers("ACGT", k = 1, start = 3:1, width = 1), cdk_ACGT))
+ stop("[countDnaKmers] Test 1 '", filename, "' FAILED!")
>
> if(!identical(countDnaKmers("ACGT", k = 1, start = 3, width = 1), cdk_ACGT_one))
+ stop("[countDnaKmers] Test 2 '", filename, "' FAILED!")
>
> if(!identical(
+ countDnaKmers("ATTNAC", k = 2, start = 1:3, width = 1), cdk_ATTNAC))
+ stop("[countDnaKmers] Test 3 '", filename, "' FAILED!")
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## revCountDnaKmers
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> if(!identical(
+ revCountDnaKmers("ACGTACGT", k = 2, start = 6:4, width = 2), rck_ACGT))
+ stop("[revCountDnaKmers] Test 1 '", filename, "' FAILED!")
>
>
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## END OF FILE
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> proc.time()
user system elapsed
0.242 0.059 0.291
seqTools.Rcheck/seqTools-Ex.timings
| name | user | system | elapsed | |
| ascii2char | 0.001 | 0.000 | 0.001 | |
| cbDistMatrix | 0.004 | 0.000 | 0.003 | |
| countDnaKmers | 0.001 | 0.000 | 0.001 | |
| countFastaKmers | 0.001 | 0.000 | 0.001 | |
| countGenomeKmers | 0.000 | 0.001 | 0.001 | |
| countSpliceKmers | 0.000 | 0.002 | 0.001 | |
| kMerIndex | 0 | 0 | 0 | |
| phredTable | 0.005 | 0.000 | 0.005 | |
| revCountDnaKmers | 0.001 | 0.000 | 0.000 | |
| simFastqqRunTimes | 0 | 0 | 0 | |
| sim_fq | 0 | 0 | 0 | |
| writeFai | 0.000 | 0.000 | 0.001 | |
| writeSimContFastq | 0.001 | 0.000 | 0.000 | |
| writeSimFastq | 0.001 | 0.000 | 0.000 | |