Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:39 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 13/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ACME 2.63.0 (landing page) Sean Davis
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
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: 2.63.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ACME.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ACME_2.63.0.tar.gz |
StartedAt: 2024-12-23 19:37:35 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 19:38:40 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 64.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ACME.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ACME.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ACME_2.63.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ACME.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘ACME/DESCRIPTION’ ... OK * this is package ‘ACME’ version ‘2.63.0’ * 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 ... WARNING Found the following significant warnings: windowChisq.c:58:21: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] windowChisq.c:63:20: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] windowChisq.c:86:20: warning: initialization of ‘void * (*)(void)’ from incompatible pointer type ‘struct SEXPREC * (*)(struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *)’ [-Wincompatible-pointer-types] See ‘/home/biocbuild/bbs-3.21-bioc/meat/ACME.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... INFO installed size is 14.1Mb sub-directories of 1Mb or more: data 3.1Mb extdata 10.6Mb * 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 loading without being on the library search path ... 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: ACMECalcSet-class.Rd: ExpressionSet-class, eSet-class, VersionedBiobase-class, Versioned-class ACMESet-class.Rd: ExpressionSet-class, eSet-class, VersionedBiobase-class, Versioned-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed findClosestGene 1.491 0.042 7.08 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/ACME.Rcheck/00check.log’ for details.
ACME.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ACME ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘ACME’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c windowChisq.c -o windowChisq.o windowChisq.c: In function ‘windowChisq’: windowChisq.c:58:21: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] 58 | firstprobe>0) { | ~~~~~~~~~~^~ windowChisq.c:63:20: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] 63 | lastprobe<(na-1)) { | ~~~~~~~~~^~~~~~~ windowChisq.c:21:11: warning: unused variable ‘xa’ [-Wunused-variable] 21 | double *xa,*xlocations,*xchivals; | ^~ windowChisq.c: At top level: windowChisq.c:86:20: warning: initialization of ‘void * (*)(void)’ from incompatible pointer type ‘struct SEXPREC * (*)(struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *, struct SEXPREC *)’ [-Wincompatible-pointer-types] 86 | {"windowChisq",&windowChisq,5}, | ^ windowChisq.c:86:20: note: (near initialization for ‘callMethods[0].fun’) gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o ACME.so windowChisq.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-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 | 1.289 | 0.074 | 1.364 | |
ACMESet-class | 0.446 | 0.022 | 0.469 | |
aGFF-class | 0.484 | 0.015 | 0.499 | |
aGFFCalc-class | 1.071 | 0.021 | 1.092 | |
do.aGFF.calc | 1.114 | 0.023 | 1.138 | |
example.agff | 0.436 | 0.012 | 0.447 | |
findClosestGene | 1.491 | 0.042 | 7.080 | |
findRegions | 1.837 | 0.059 | 1.896 | |
generics | 0.432 | 0.013 | 0.446 | |
getRefflat | 1.306 | 0.026 | 2.084 | |
read.resultsGFF | 2.692 | 0.086 | 2.781 | |
write.bedGraph | 1.333 | 0.024 | 1.357 | |
write.sgr | 1.051 | 0.029 | 1.081 | |