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 12:05 -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 13/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ACME 2.62.0 (landing page) Sean Davis
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | 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 ACME package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ACME.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: ACME |
Version: 2.62.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ACME.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ACME_2.62.0.tar.gz |
StartedAt: 2024-12-19 23:30:11 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 23:31:53 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 102.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ACME.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ACME.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ACME_2.62.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ACME.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ACME/DESCRIPTION’ ... OK * this is package ‘ACME’ version ‘2.62.0’ * 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 ‘ACME’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 30.8Mb sub-directories of 1Mb or more: data 3.1Mb extdata 27.3Mb * 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 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 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 ... NOTE .plotACMECalcSet: no visible global function definition for ‘par’ .plotACMECalcSet: no visible global function definition for ‘axis’ .plotACMECalcSet: no visible global function definition for ‘abline’ .plotACMESet: no visible global function definition for ‘par’ do.aGFF.calc: no visible global function definition for ‘quantile’ findClosestGene: no visible binding for global variable ‘refflat’ findClosestGene: no visible binding for '<<-' assignment to ‘refflat’ findRegions : <anonymous>: no visible global function definition for ‘median’ getRefflat: no visible global function definition for ‘download.file’ getRefflat: no visible global function definition for ‘read.delim’ plotgff: no visible global function definition for ‘par’ plotgffcalc: no visible global function definition for ‘par’ plotgffcalc: no visible global function definition for ‘axis’ plotgffcalc: no visible global function definition for ‘abline’ read.resultsGFF: no visible global function definition for ‘read.delim’ windowChisq: no visible global function definition for ‘pchisq’ write.bedGraph: no visible global function definition for ‘write.table’ write.sgr: no visible global function definition for ‘write.table’ plot,ACMECalcSet: no visible global function definition for ‘par’ plot,ACMECalcSet: no visible global function definition for ‘axis’ plot,ACMECalcSet: no visible global function definition for ‘abline’ plot,ACMESet: no visible global function definition for ‘par’ plot,aGFF: no visible global function definition for ‘par’ plot,aGFFCalc: no visible global function definition for ‘par’ plot,aGFFCalc: no visible global function definition for ‘axis’ plot,aGFFCalc: no visible global function definition for ‘abline’ Undefined global functions or variables: abline axis download.file median par pchisq quantile read.delim refflat write.table Consider adding importFrom("graphics", "abline", "axis", "par") importFrom("stats", "median", "pchisq", "quantile") importFrom("utils", "download.file", "read.delim", "write.table") 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 ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ACME.Rcheck/00check.log’ for details.
ACME.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ACME ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘ACME’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c windowChisq.c -o windowChisq.o windowChisq.c:57:71: warning: & has lower precedence than >; > will be evaluated first [-Wparentheses] while((xlocations[i]-xlocations[firstprobe-1] < (halfWindowSize)) & ^ windowChisq.c:57:71: note: place parentheses around the '>' expression to silence this warning while((xlocations[i]-xlocations[firstprobe-1] < (halfWindowSize)) & ^ windowChisq.c:57:71: note: place parentheses around the & expression to evaluate it first while((xlocations[i]-xlocations[firstprobe-1] < (halfWindowSize)) & ^ ( windowChisq.c:62:70: warning: & has lower precedence than <; < will be evaluated first [-Wparentheses] while((xlocations[lastprobe+1]-xlocations[i] < (halfWindowSize)) & ^ windowChisq.c:62:70: note: place parentheses around the '<' expression to silence this warning while((xlocations[lastprobe+1]-xlocations[i] < (halfWindowSize)) & ^ windowChisq.c:62:70: note: place parentheses around the & expression to evaluate it first while((xlocations[lastprobe+1]-xlocations[i] < (halfWindowSize)) & ^ ( windowChisq.c:21:11: warning: unused variable 'xa' [-Wunused-variable] double *xa,*xlocations,*xchivals; ^ windowChisq.c:86:20: warning: incompatible function pointer types initializing 'DL_FUNC' (aka 'void *(*)(void)') with an expression of type 'SEXP (*)(SEXP, SEXP, SEXP, SEXP, SEXP)' (aka 'struct SEXPREC *(*)(struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *)') [-Wincompatible-function-pointer-types] {"windowChisq",&windowChisq,5}, ^~~~~~~~~~~~ 4 warnings generated. clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ACME.so windowChisq.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-ACME/00new/ACME/libs ** R ** data ** 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 (ACME)
ACME.Rcheck/ACME-Ex.timings
name | user | system | elapsed | |
ACMECalcSet-class | 2.320 | 0.159 | 2.571 | |
ACMESet-class | 0.756 | 0.024 | 0.788 | |
aGFF-class | 0.704 | 0.016 | 0.730 | |
aGFFCalc-class | 1.994 | 0.097 | 2.131 | |
do.aGFF.calc | 1.984 | 0.097 | 2.104 | |
example.agff | 0.705 | 0.014 | 0.726 | |
findClosestGene | 2.429 | 0.156 | 3.355 | |
findRegions | 3.848 | 0.157 | 4.153 | |
generics | 0.664 | 0.013 | 0.679 | |
getRefflat | 2.002 | 0.119 | 2.737 | |
read.resultsGFF | 4.556 | 0.145 | 4.748 | |
write.bedGraph | 3.382 | 0.205 | 3.650 | |
write.sgr | 2.922 | 0.180 | 3.217 | |