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This page was generated on 2024-02-22 12:48:22 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
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Package 1909/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqTools 1.37.0  (landing page)
Wolfgang Kaisers
Snapshot Date: 2024-02-21 14:10:10 -0500 (Wed, 21 Feb 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 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for seqTools on nebbiolo1


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.

raw results


Summary

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: 2024-02-22 02:57:17 -0500 (Thu, 22 Feb 2024)
EndedAt: 2024-02-22 02:57:43 -0500 (Thu, 22 Feb 2024)
EllapsedTime: 26.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: seqTools.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### 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) (2024-01-16 r85808)
* 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 22.04.3 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 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 ... 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.



Installation output

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)

Tests output

seqTools.Rcheck/tests/test-all.Rout


R Under development (unstable) (2024-01-16 r85808) -- "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 
  0.197   0.071   0.257 

seqTools.Rcheck/tests/test_seqTools.Rout


R Under development (unstable) (2024-01-16 r85808) -- "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 
  0.246   0.038   0.271 

Example timings

seqTools.Rcheck/seqTools-Ex.timings

nameusersystemelapsed
ascii2char0.0010.0000.001
cbDistMatrix0.0030.0000.004
countDnaKmers0.0010.0000.001
countFastaKmers0.0010.0000.001
countGenomeKmers0.0000.0010.001
countSpliceKmers0.0000.0020.002
kMerIndex000
phredTable0.0050.0000.004
revCountDnaKmers0.0010.0000.001
simFastqqRunTimes0.0010.0000.000
sim_fq000
writeFai000
writeSimContFastq000
writeSimFastq0.0010.0000.001