Wolfgang Kaisers
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/seqTools |
| git_branch: RELEASE_3_17 |
| git_last_commit: 737a565 |
| git_last_commit_date: 2023-04-25 10:36:30 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:12 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1895/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| seqTools 1.34.0 (landing page) Wolfgang Kaisers
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the seqTools package: - 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: 1.34.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqTools_1.34.0.tar.gz |
| StartedAt: 2023-10-19 00:28:15 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 00:29:24 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 68.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: seqTools.Rcheck |
| Warnings: 3 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqTools_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/seqTools.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqTools’ version ‘1.34.0’
* 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 ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/libs/seqTools.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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/seqTools/extdata’, resetting
Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 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: 3 WARNINGs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/seqTools.Rcheck/00check.log’
for details.
seqTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL seqTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘seqTools’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c seqTools.c -o seqTools.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o seqTools.so seqTools.o -lm -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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.
>
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## 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) '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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) '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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) '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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) '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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) '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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) '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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
0.304 0.079 0.728
seqTools.Rcheck/tests/test_seqTools.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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.
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## 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
0.303 0.079 0.726
seqTools.Rcheck/seqTools-Ex.timings
| name | user | system | elapsed | |
| ascii2char | 0.000 | 0.001 | 0.003 | |
| cbDistMatrix | 0.005 | 0.002 | 0.009 | |
| countDnaKmers | 0.000 | 0.001 | 0.000 | |
| countFastaKmers | 0.001 | 0.001 | 0.006 | |
| countGenomeKmers | 0.000 | 0.000 | 0.001 | |
| countSpliceKmers | 0.001 | 0.001 | 0.002 | |
| kMerIndex | 0 | 0 | 0 | |
| phredTable | 0.003 | 0.002 | 0.012 | |
| revCountDnaKmers | 0.001 | 0.000 | 0.001 | |
| simFastqqRunTimes | 0.000 | 0.000 | 0.001 | |
| sim_fq | 0.000 | 0.000 | 0.001 | |
| writeFai | 0 | 0 | 0 | |
| writeSimContFastq | 0.001 | 0.000 | 0.000 | |
| writeSimFastq | 0.001 | 0.000 | 0.001 | |