Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 866/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
girafe 1.58.0 (landing page) J. Toedling
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the girafe package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/girafe.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: girafe |
Version: 1.58.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:girafe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings girafe_1.58.0.tar.gz |
StartedAt: 2024-12-20 21:05:11 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 21:09:51 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 280.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: girafe.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:girafe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings girafe_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/girafe.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘girafe/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘girafe’ version ‘1.58.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'Rsamtools', 'intervals', 'ShortRead', 'genomeIntervals', 'grid' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘girafe’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ ‘genomeIntervals’ A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 whether startup messages can be suppressed ... NOTE No methods found in package ‘IRanges’ for requests: ‘score’, ‘score<-’, ‘sort’ when loading ‘girafe’ It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘MASS’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: ‘Rsamtools’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported object imported by a ':::' call: ‘genomeIntervals:::intervalsForOverlap’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE agiFromBam: no visible binding for global variable ‘mclapply’ agiFromBam: no visible global function definition for ‘scanBamHeader’ agiFromBam: no visible global function definition for ‘ScanBamParam’ agiFromBam : <anonymous>: no visible global function definition for ‘scanBamFlag’ agiFromBam : <anonymous>: no visible global function definition for ‘scanBam’ countReadsAnnotated: no visible binding for global variable ‘mclapply’ countReadsAnnotated: no visible binding for global variable ‘fraction1’ fracOverlap: no visible binding for global variable ‘fraction1’ fracOverlap: no visible binding for global variable ‘fraction2’ getFeatureCounts: no visible binding for global variable ‘fraction1’ getFeatureCounts: no visible binding for global variable ‘Index1’ intPhred: no visible binding for global variable ‘mclapply’ oldAGIoverlap: no visible binding for global variable ‘mclapply’ plotReads: no visible binding for global variable ‘x.start’ plotReads: no visible binding for global variable ‘x.end’ plotReads: no visible binding for global variable ‘y’ reduceOne: no visible binding for global variable ‘fraction1’ reduceOne: no visible binding for global variable ‘fraction2’ windowCountAndGC: no visible binding for global variable ‘n.reads’ windowCountAndGC: no visible global function definition for ‘unmasked’ clusters,AlignedGenomeIntervals: no visible binding for global variable ‘mclapply’ clusters,Genome_intervals: no visible binding for global variable ‘mclapply’ coverage,AlignedGenomeIntervals: no visible binding for global variable ‘mclapply’ coverage,AlignedGenomeIntervals : <anonymous>: no visible binding for global variable ‘on.minus’ interval_included,AlignedGenomeIntervals-AlignedGenomeIntervals: no visible binding for global variable ‘mclapply’ reduce,AlignedGenomeIntervals: no visible binding for global variable ‘mclapply’ reduce,Genome_intervals: no visible binding for global variable ‘mclapply’ reduce,Genome_intervals: no visible binding for global variable ‘fraction1’ reduce,Genome_intervals: no visible binding for global variable ‘fraction2’ Undefined global functions or variables: Index1 ScanBamParam fraction1 fraction2 mclapply n.reads on.minus scanBam scanBamFlag scanBamHeader unmasked x.end x.start y * 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 for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed AlignedGenomeIntervals-class 8.235 0.109 8.347 perWindow 7.508 0.291 7.804 negbinomsig 7.323 0.286 7.652 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 6 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/girafe.Rcheck/00check.log’ for details.
girafe.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL girafe ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘girafe’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c coverage.cpp -o coverage.o coverage.cpp:2:17: warning: using directive refers to implicitly-defined namespace 'std' using namespace std; ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c girafe_init.c -o girafe_init.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o girafe.so coverage.o girafe_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-girafe/00new/girafe/libs ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘IRanges’ for requests: ‘score’, ‘score<-’, ‘sort’ when loading ‘girafe’ Creating a generic function for ‘sample’ from package ‘base’ in package ‘girafe’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘IRanges’ for requests: ‘score’, ‘score<-’, ‘sort’ when loading ‘girafe’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location No methods found in package ‘IRanges’ for requests: ‘score’, ‘score<-’, ‘sort’ when loading ‘girafe’ ** testing if installed package keeps a record of temporary installation path * DONE (girafe)
girafe.Rcheck/girafe-Ex.timings
name | user | system | elapsed | |
AlignedGenomeIntervals-class | 8.235 | 0.109 | 8.347 | |
agiFromBam | 0.214 | 0.004 | 0.218 | |
countReadsAnnotated | 0.079 | 0.001 | 0.079 | |
fracOverlap | 0.253 | 0.005 | 0.259 | |
intPhred | 0.074 | 0.205 | 0.281 | |
medianByPosition | 0.308 | 0.169 | 0.478 | |
negbinomsig | 7.323 | 0.286 | 7.652 | |
perWindow | 7.508 | 0.291 | 7.804 | |
plotAligned | 0.020 | 0.001 | 0.021 | |
trimAdapter | 0.086 | 0.192 | 0.278 | |
weightedConsensusMatrix | 0.003 | 0.000 | 0.003 | |
whichNearestMethods | 0.302 | 0.211 | 0.513 | |