| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-06-06 11:00:31 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
|
To the developers/maintainers of the FastqCleaner package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FastqCleaner.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 673/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FastqCleaner 1.19.0 (landing page) Leandro Roser
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: FastqCleaner |
| Version: 1.19.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:FastqCleaner.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings FastqCleaner_1.19.0.tar.gz |
| StartedAt: 2023-06-05 22:19:45 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 22:24:48 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 302.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FastqCleaner.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:FastqCleaner.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings FastqCleaner_1.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/FastqCleaner.Rcheck’
* using R version 4.3.0 (2023-04-21)
* 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
* checking for file ‘FastqCleaner/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FastqCleaner’ version ‘1.19.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following non-portable file paths:
FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-11-1.png
FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-12-1.png
FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-13-1.png
FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-14-1.png
FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-7-1.png
FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-8-1.png
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FastqCleaner’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 6.7Mb
sub-directories of 1Mb or more:
application 4.3Mb
libs 2.2Mb
* 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 ... 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 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘Overview.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/FastqCleaner.Rcheck/00check.log’
for details.
FastqCleaner.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL FastqCleaner ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘FastqCleaner’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c cpp_GC_content.cpp -o cpp_GC_content.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c cpp_base_content.cpp -o cpp_base_content.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c cpp_check_quality_threshold.cpp -o cpp_check_quality_threshold.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c cpp_create_stringvec.cpp -o cpp_create_stringvec.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c cpp_which_true.cpp -o cpp_which_true.o g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o FastqCleaner.so RcppExports.o cpp_GC_content.o cpp_base_content.o cpp_check_quality_threshold.o cpp_create_stringvec.o cpp_which_true.o -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/site-library/00LOCK-FastqCleaner/00new/FastqCleaner/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 (FastqCleaner)
FastqCleaner.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> library(testthat)
> library(FastqCleaner)
>
> test_check("FastqCleaner")
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 0 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (10)
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 0 ]
>
> proc.time()
user system elapsed
12.875 1.070 13.962
FastqCleaner.Rcheck/FastqCleaner-Ex.timings
| name | user | system | elapsed | |
| adapter_filter | 0.386 | 0.039 | 0.427 | |
| check_encoding | 0.162 | 0.020 | 0.183 | |
| complex_filter | 0.430 | 0.016 | 0.447 | |
| fixed_filter | 0.365 | 0.012 | 0.378 | |
| inject_letter_random | 0.218 | 0.000 | 0.219 | |
| launch_fqc | 0 | 0 | 0 | |
| length_filter | 0.299 | 0.012 | 0.312 | |
| matching | 0.193 | 0.012 | 0.205 | |
| n_filter | 0.559 | 0.040 | 0.601 | |
| qmean_filter | 0.329 | 0.012 | 0.342 | |
| random_length | 0.039 | 0.000 | 0.039 | |
| random_qual | 0.022 | 0.000 | 0.022 | |
| random_seq | 0.039 | 0.000 | 0.040 | |
| seq_filter | 0.306 | 0.008 | 0.315 | |
| seq_names | 0.036 | 0.000 | 0.036 | |
| trim3q_filter | 0.352 | 0.000 | 0.353 | |
| unique_filter | 0.29 | 0.00 | 0.29 | |