Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:39 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the hummingbird package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hummingbird.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 881/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
hummingbird 1.2.0 (landing page) Eleni Adam
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: hummingbird |
Version: 1.2.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:hummingbird.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hummingbird_1.2.0.tar.gz |
StartedAt: 2021-10-14 20:04:45 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 20:07:25 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 159.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: hummingbird.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:hummingbird.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hummingbird_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/hummingbird.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘hummingbird/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘hummingbird’ version ‘1.2.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘hummingbird’ 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 ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... 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 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-3.13-bioc/meat/hummingbird.Rcheck/00check.log’ for details.
hummingbird.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL hummingbird ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘hummingbird’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c em.cpp -o em.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c init.cpp -o init.o init.cpp:11:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] NULL ^~~~ { } /Library/Developer/CommandLineTools/usr/lib/clang/10.0.1/include/stddef.h:100:18: note: expanded from macro 'NULL' # define NULL __null ^~~~~~ 1 warning generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c postAdjustment.cpp -o postAdjustment.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 hummingbird.so RcppExports.o em.o init.o postAdjustment.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-hummingbird/00new/hummingbird/libs ** R ** data *** moving datasets to lazyload DB ** 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 (hummingbird)
hummingbird.Rcheck/hummingbird-Ex.timings
name | user | system | elapsed | |
abnormM | 0.043 | 0.149 | 0.191 | |
abnormUM | 0.044 | 0.168 | 0.212 | |
exampleHummingbird | 0.166 | 0.020 | 0.188 | |
exampleSECase | 0.221 | 0.016 | 0.238 | |
exampleSEControl | 0.203 | 0.014 | 0.216 | |
hummingbirdEM | 1.498 | 0.056 | 1.556 | |
hummingbirdEMinternal | 0.927 | 0.014 | 0.942 | |
hummingbirdGraph | 1.295 | 0.019 | 1.315 | |
hummingbirdPostAdjustment | 1.629 | 0.019 | 1.651 | |
hummingbirdPostAdjustmentInternal | 1.031 | 0.019 | 1.055 | |
normM | 0.043 | 0.144 | 0.255 | |
normUM | 0.051 | 0.181 | 0.232 | |
pos | 0.016 | 0.057 | 0.074 | |