Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:27 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 SMAP package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SMAP.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1902/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SMAP 1.62.0 (landing page) Robin Andersson
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: SMAP |
Version: 1.62.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SMAP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SMAP_1.62.0.tar.gz |
StartedAt: 2023-04-10 22:46:33 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 22:47:12 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 39.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SMAP.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SMAP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SMAP_1.62.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/SMAP.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SMAP/DESCRIPTION’ ... OK * this is package ‘SMAP’ version ‘1.62.0’ * 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 ‘SMAP’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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' call to ‘methods’ which was already attached by Depends. Please remove these calls from your code. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘SMAP/R/AllClasses.R’: .onLoad calls: require("methods", quietly = TRUE) Package startup functions should not change the search path. See section ‘Good practice’ in '?.onAttach'. .draw.dist,gaussparam: no visible global function definition for ‘abline’ plot,SMAPObservations-missing: no visible global function definition for ‘par’ plot,SMAPObservations-missing: no visible global function definition for ‘points’ plot,SMAPObservations-missing: no visible global function definition for ‘abline’ plot,SMAPObservations-missing: no visible global function definition for ‘box’ plot,SMAPObservations-missing: no visible global function definition for ‘axis’ profilePlot,SMAPProfile: no visible global function definition for ‘par’ profilePlot,SMAPProfile: no visible global function definition for ‘points’ profilePlot,SMAPProfile: no visible global function definition for ‘abline’ profilePlot,SMAPProfile: no visible global function definition for ‘box’ profilePlot,SMAPProfile: no visible global function definition for ‘axis’ profilePlot,SMAPProfiles: no visible global function definition for ‘par’ profilePlot,SMAPProfiles: no visible global function definition for ‘abline’ profilePlot,SMAPProfiles: no visible global function definition for ‘box’ profilePlot,SMAPProfiles: no visible global function definition for ‘axis’ Undefined global functions or variables: abline axis box par points Consider adding importFrom("graphics", "abline", "axis", "box", "par", "points") to your NAMESPACE file. * 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 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 sizes of PDF files under ‘inst/doc’ ... OK * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.16-bioc/meat/SMAP.Rcheck/00check.log’ for details.
SMAP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SMAP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘SMAP’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c gradient.c -o gradient.o gradient.c:142:7: warning: variable 'lower' set but not used [-Wunused-but-set-variable] int lower; ^ gradient.c:247:10: warning: unused variable 'tmp' [-Wunused-variable] double tmp; ^ 2 warnings generated. clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c overlap.c -o overlap.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c prob.c -o prob.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c viterbi.c -o viterbi.o clang -mmacosx-version-min=10.13 -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 SMAP.so gradient.o init.o overlap.o prob.o viterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-SMAP/00new/SMAP/libs ** R ** data ** 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 (SMAP)
SMAP.Rcheck/SMAP-Ex.timings
name | user | system | elapsed | |
GBM | 0.373 | 0.040 | 0.416 | |
SMAPObservations | 1.682 | 0.068 | 1.758 | |
smap | 4.478 | 0.108 | 4.591 | |