Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:54:20 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE ACME PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 14/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ACME 2.44.0 Sean Davis
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK |
Package: ACME |
Version: 2.44.0 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ACME.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ACME_2.44.0.tar.gz |
StartedAt: 2020-10-16 22:38:39 -0400 (Fri, 16 Oct 2020) |
EndedAt: 2020-10-16 22:39:54 -0400 (Fri, 16 Oct 2020) |
EllapsedTime: 75.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ACME.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ACME.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ACME_2.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/ACME.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ACME/DESCRIPTION’ ... OK * this is package ‘ACME’ version ‘2.44.0’ * 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:58:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] windowChisq.c:63:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] windowChisq.c:86:20: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types] See ‘/home/biocbuild/bbs-3.11-bioc/meat/ACME.Rcheck/00install.out’ for details. * 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 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 ... 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 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: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.11-bioc/meat/ACME.Rcheck/00check.log’ for details.
ACME.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL ACME ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘ACME’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c windowChisq.c -o windowChisq.o windowChisq.c: In function ‘windowChisq’: windowChisq.c:58:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] firstprobe>0) { ~~~~~~~~~~^~ windowChisq.c:63:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] lastprobe<(na-1)) { ~~~~~~~~~^~~~~~~ windowChisq.c:21:11: warning: unused variable ‘xa’ [-Wunused-variable] double *xa,*xlocations,*xchivals; ^~ windowChisq.c: At top level: windowChisq.c:86:20: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types] {"windowChisq",&windowChisq,5}, ^ windowChisq.c:86:20: note: (near initialization for ‘callMethods[0].fun’) gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o ACME.so windowChisq.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-bioc/R/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 | 1.549 | 0.040 | 1.589 | |
ACMESet-class | 0.636 | 0.004 | 0.640 | |
aGFF-class | 0.725 | 0.012 | 0.737 | |
aGFFCalc-class | 1.340 | 0.004 | 1.344 | |
do.aGFF.calc | 1.229 | 0.016 | 1.244 | |
example.agff | 0.777 | 0.012 | 0.789 | |
findClosestGene | 1.713 | 0.051 | 4.703 | |
findRegions | 3.526 | 0.028 | 3.554 | |
generics | 0.464 | 0.000 | 0.465 | |
getRefflat | 1.484 | 0.036 | 4.072 | |
read.resultsGFF | 3.314 | 0.032 | 3.403 | |
write.bedGraph | 2.666 | 0.052 | 2.718 | |
write.sgr | 2.350 | 0.027 | 2.377 | |