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This page was generated on 2021-05-06 12:35:55 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the NanoMethViz package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1197/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
NanoMethViz 1.0.0 (landing page) Shian Su
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: NanoMethViz |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NanoMethViz_1.0.0.tar.gz |
StartedAt: 2021-05-06 04:07:36 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 04:16:11 -0400 (Thu, 06 May 2021) |
EllapsedTime: 514.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: NanoMethViz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NanoMethViz.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NanoMethViz_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/NanoMethViz.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘NanoMethViz/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘NanoMethViz’ version ‘1.0.0’ * 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 ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘NanoMethViz’ can be installed ... OK * 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 ... NOTE 'library' or 'require' calls in package code: ‘Homo.sapiens’ ‘Mus.musculus’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * 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 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_gene 40.189 1.413 41.671 plot_region 39.237 1.165 40.842 NanoMethResult-class 25.322 2.000 29.539 plot_grange 19.820 0.585 20.435 query_methy 19.544 0.457 20.056 load_example_nanomethresult 18.315 0.492 18.838 get_exons_mus_musculus 17.333 0.839 18.205 get_exons_homo_sapiens 17.055 1.015 18.100 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.12-bioc/meat/NanoMethViz.Rcheck/00check.log’ for details.
NanoMethViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NanoMethViz ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘NanoMethViz’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable] SEXP data = Parent::get__(); ^ 1 warning generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c convert_methy_to_dss.cpp -o convert_methy_to_dss.o In file included from convert_methy_to_dss.cpp:1: In file included from ./convert_methy_to_dss.h:2: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable] SEXP data = Parent::get__(); ^ 1 warning generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o In file included from utils.cpp:1: In file included from ./utils.h:2: In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable] SEXP data = Parent::get__(); ^ 1 warning generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o NanoMethViz.so RcppExports.o convert_methy_to_dss.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-NanoMethViz/00new/NanoMethViz/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 (NanoMethViz)
NanoMethViz.Rcheck/NanoMethViz-Ex.timings
name | user | system | elapsed | |
NanoMethResult-class | 25.322 | 2.000 | 29.539 | |
bsseq_to_edger | 0.985 | 0.031 | 1.025 | |
bsseq_to_log_methy_ratio | 0.916 | 0.016 | 0.935 | |
create_tabix_file | 0.183 | 0.018 | 0.204 | |
exons | 0.002 | 0.000 | 0.002 | |
get_exons_homo_sapiens | 17.055 | 1.015 | 18.100 | |
get_exons_mus_musculus | 17.333 | 0.839 | 18.205 | |
load_example_nanomethresult | 18.315 | 0.492 | 18.838 | |
methy | 0.001 | 0.001 | 0.002 | |
methy_col_names | 0.001 | 0.000 | 0.000 | |
methy_to_bsseq | 1.080 | 0.021 | 1.102 | |
plot_gene | 40.189 | 1.413 | 41.671 | |
plot_grange | 19.820 | 0.585 | 20.435 | |
plot_region | 39.237 | 1.165 | 40.842 | |
query_methy | 19.544 | 0.457 | 20.056 | |
samples | 0.001 | 0.000 | 0.001 | |