Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:14 -0400 (Fri, 20 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
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 2145/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
trio 3.38.0 (landing page) Holger Schwender
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | ![]() | |||||||
To the developers/maintainers of the trio package: - 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: trio |
Version: 3.38.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:trio.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings trio_3.38.0.tar.gz |
StartedAt: 2023-10-19 08:29:48 -0400 (Thu, 19 Oct 2023) |
EndedAt: 2023-10-19 08:34:48 -0400 (Thu, 19 Oct 2023) |
EllapsedTime: 300.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: trio.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:trio.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings trio_3.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/trio.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * 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 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘trio/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘trio’ version ‘3.38.0’ * 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 ‘trio’ can be installed ... OK * checking installed package size ... OK * 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 startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function call to a different package: .C("clogreg", ..., PACKAGE = "LogicReg") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... OK * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed print.trioFS 5.976 0.067 10.708 trioFS 5.727 0.068 10.390 trio.permTest 5.258 0.069 9.523 colGxGPerms 5.198 0.085 9.429 plot.trioLR 3.995 0.157 7.443 * 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 NOTE See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/trio.Rcheck/00check.log’ for details.
trio.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL trio ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘trio’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (trio)
trio.Rcheck/trio-Ex.timings
name | user | system | elapsed | |
allelicTDT | 0.028 | 0.005 | 0.070 | |
colEMlrt | 0.114 | 0.005 | 0.208 | |
colGxE | 0.008 | 0.001 | 0.015 | |
colGxGPerms | 5.198 | 0.085 | 9.429 | |
colPOlrt | 0.017 | 0.002 | 0.034 | |
colTDTmaxTest | 0.041 | 0.004 | 0.086 | |
colTDTsam | 0.039 | 0.006 | 0.080 | |
findLDblocks | 0.030 | 0.003 | 0.061 | |
getLD | 0.015 | 0.002 | 0.034 | |
getMatPseudo | 0.007 | 0.001 | 0.016 | |
lrControl | 0.001 | 0.000 | 0.005 | |
ped2geno | 0.000 | 0.001 | 0.000 | |
plot.LDblocks | 0.211 | 0.006 | 0.376 | |
plot.getLD | 0.029 | 0.004 | 0.059 | |
plot.trioLR | 3.995 | 0.157 | 7.443 | |
poly4root | 0 | 0 | 0 | |
print.colGxE | 0.051 | 0.006 | 0.094 | |
print.trioFS | 5.976 | 0.067 | 10.708 | |
print.trioLR | 2.671 | 0.031 | 4.832 | |
probTDT | 0.042 | 0.017 | 0.104 | |
read.pedfile | 0 | 0 | 0 | |
removeSNPs | 0.006 | 0.001 | 0.012 | |
scoreTDT | 0.022 | 0.002 | 0.043 | |
tdt | 0.023 | 0.003 | 0.048 | |
tdtGxG | 1.693 | 0.020 | 3.051 | |
trio.check | 0.717 | 0.024 | 1.352 | |
trio.data | 0.004 | 0.001 | 0.008 | |
trio.permTest | 5.258 | 0.069 | 9.523 | |
trio.power | 0.013 | 0.001 | 0.023 | |
trio.prepare | 2.493 | 0.039 | 4.544 | |
trio.sim | 0.338 | 0.005 | 0.618 | |
trioFS | 5.727 | 0.068 | 10.390 | |
trioLR | 2.596 | 0.031 | 4.668 | |