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This page was generated on 2021-10-15 15:06:27 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the ACME package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 14/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ACME 2.48.0 (landing page) Sean Davis
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 2.48.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ACME.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ACME_2.48.0.tar.gz |
StartedAt: 2021-10-14 16:05:29 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 16:06:50 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 81.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ACME.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ACME.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ACME_2.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ACME.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ACME/DESCRIPTION’ ... OK * this is package ‘ACME’ version ‘2.48.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ACME’ can be installed ... OK * 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 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 findClosestGene 1.904 0.102 8.098 getRefflat 1.810 0.101 7.258 * 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-3.13-bioc/meat/ACME.Rcheck/00check.log’ for details.
ACME.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ACME ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘ACME’ ... ** 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 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 *(*)()') 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 -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 ACME.so windowChisq.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/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 | 1.747 | 0.100 | 1.847 | |
ACMESet-class | 0.576 | 0.013 | 0.590 | |
aGFF-class | 0.565 | 0.020 | 0.585 | |
aGFFCalc-class | 1.302 | 0.060 | 1.361 | |
do.aGFF.calc | 1.464 | 0.070 | 1.535 | |
example.agff | 0.504 | 0.010 | 0.514 | |
findClosestGene | 1.904 | 0.102 | 8.098 | |
findRegions | 3.089 | 0.107 | 3.197 | |
generics | 0.603 | 0.008 | 0.611 | |
getRefflat | 1.810 | 0.101 | 7.258 | |
read.resultsGFF | 3.704 | 0.092 | 3.799 | |
write.bedGraph | 2.208 | 0.130 | 2.348 | |
write.sgr | 2.067 | 0.107 | 2.182 | |