Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-06-24 12:07:45 -0400 (Fri, 24 Jun 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" | 4380 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" | 4156 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" | 4221 |
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 |
To the developers/maintainers of the methylclock package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylclock.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1149/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methylclock 1.2.0 (landing page) Dolors Pelegri-Siso
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: methylclock |
Version: 1.2.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylclock.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylclock_1.2.0.tar.gz |
StartedAt: 2022-06-24 05:03:15 -0400 (Fri, 24 Jun 2022) |
EndedAt: 2022-06-24 05:19:36 -0400 (Fri, 24 Jun 2022) |
EllapsedTime: 981.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: methylclock.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylclock.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylclock_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/methylclock.Rcheck’ * using R version 4.2.0 (2022-04-22) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘methylclock/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘methylclock’ version ‘1.2.0’ * package encoding: UTF-8 * 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 ‘methylclock’ 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 dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘planet’ All declared Imports should be used. Unexported object imported by a ':::' call: ‘minfi:::projectCellType’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE DNAmAge: no visible binding for global variable ‘coefHorvath’ DNAmAge: no visible binding for global variable ‘coefHannum’ DNAmAge: no visible binding for global variable ‘coefLevine’ DNAmAge: no visible binding for global variable ‘coefSkin’ DNAmAge: no visible binding for global variable ‘coefPedBE’ DNAmAge: no visible binding for global variable ‘coefWu’ DNAmAge: no visible binding for global variable ‘coefTL’ DNAmAge: no visible binding for global variable ‘coefBLUP’ DNAmAge: no visible binding for global variable ‘coefEN’ DNAmGA: no visible binding for global variable ‘coefKnightGA’ DNAmGA: no visible binding for global variable ‘coefBohlin’ DNAmGA: no visible binding for global variable ‘coefMayneGA’ DNAmGA: no visible binding for global variable ‘coefLeeGA’ DNAmGA: no visible binding for global variable ‘coefEPIC’ DNAmGA: no visible global function definition for ‘meffil.estimate.cell.counts.from.betas’ DNAmGA: no visible global function definition for ‘install.packages’ DNAmGA: no visible global function definition for ‘data’ DNAmGA: no visible binding for global variable ‘plCellCpGsThird’ checkClocks: no visible binding for global variable ‘MethylationData’ checkClocks: no visible binding for global variable ‘coefHorvath’ checkClocks: no visible binding for global variable ‘coefHannum’ checkClocks: no visible binding for global variable ‘coefLevine’ checkClocks: no visible binding for global variable ‘coefSkin’ checkClocks: no visible binding for global variable ‘coefPedBE’ checkClocks: no visible binding for global variable ‘coefWu’ checkClocks: no visible binding for global variable ‘coefTL’ checkClocks: no visible binding for global variable ‘coefBLUP’ checkClocks: no visible binding for global variable ‘coefEN’ checkClocksGA: no visible binding for global variable ‘coefKnightGA’ checkClocksGA: no visible binding for global variable ‘coefBohlin’ checkClocksGA: no visible binding for global variable ‘coefMayneGA’ checkClocksGA: no visible binding for global variable ‘coefLeeGA’ checkClocksGA: no visible binding for global variable ‘coefEPIC’ cpgs_imputation: no visible binding for global variable ‘cpgs.in’ plotCorClocks: no visible binding for global variable ‘method’ plotCorClocks: no visible binding for global variable ‘clock’ plotCorClocks: no visible binding for global variable ‘age’ plotCorClocks: no visible binding for global variable ‘..rr.label..’ plotCorClocks: no visible binding for global variable ‘..p.label..’ plotDNAmAge: no visible binding for global variable ‘..eq.label..’ plotDNAmAge: no visible binding for global variable ‘..rr.label..’ Undefined global functions or variables: ..eq.label.. ..p.label.. ..rr.label.. MethylationData age clock coefBLUP coefBohlin coefEN coefEPIC coefHannum coefHorvath coefKnightGA coefLeeGA coefLevine coefMayneGA coefPedBE coefSkin coefTL coefWu cpgs.in data install.packages meffil.estimate.cell.counts.from.betas method plCellCpGsThird Consider adding importFrom("utils", "data", "install.packages") 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed commonClockCpgs 58.165 1.875 67.823 DNAmAge 46.973 2.422 53.407 checkClocks 41.162 1.915 54.716 plotDNAmAge 40.441 1.321 46.656 load_DNAm_Clocks_data 35.439 1.080 40.273 load_DNAmGA_Clocks_data 32.196 1.184 37.656 checkClocksGA 21.783 0.794 25.751 DNAmGA 21.173 0.825 24.273 meffilEstimateCellCountsFromBetas 13.679 0.259 14.933 getCellTypeReference 10.144 1.857 12.800 meffilListCellTypeReferences 8.483 0.164 9.076 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.15-bioc/meat/methylclock.Rcheck/00check.log’ for details.
methylclock.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL methylclock ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘methylclock’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c NewModel1Clean.cpp -o NewModel1Clean.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c NewModel1Clean_emxAPI.cpp -o NewModel1Clean_emxAPI.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c NewModel1Clean_emxutil.cpp -o NewModel1Clean_emxutil.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c NewModel1Clean_initialize.cpp -o NewModel1Clean_initialize.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c NewModel1Clean_terminate.cpp -o NewModel1Clean_terminate.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bsxfun.cpp -o bsxfun.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c main.cpp -o main.o main.cpp:37:14: warning: unused function 'argInit_real_T' [-Wunused-function] static float argInit_real_T() ^ 1 warning generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c repmat.cpp -o repmat.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rtGetInf.cpp -o rtGetInf.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rtGetNaN.cpp -o rtGetNaN.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rt_nonfinite.cpp -o rt_nonfinite.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 methylclock.so NewModel1Clean.o NewModel1Clean_emxAPI.o NewModel1Clean_emxutil.o NewModel1Clean_initialize.o NewModel1Clean_terminate.o RcppExports.o bsxfun.o main.o repmat.o rtGetInf.o rtGetNaN.o rt_nonfinite.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-methylclock/00new/methylclock/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 (methylclock)
methylclock.Rcheck/methylclock-Ex.timings
name | user | system | elapsed | |
DNAmAge | 46.973 | 2.422 | 53.407 | |
DNAmGA | 21.173 | 0.825 | 24.273 | |
checkClocks | 41.162 | 1.915 | 54.716 | |
checkClocksGA | 21.783 | 0.794 | 25.751 | |
commonClockCpgs | 58.165 | 1.875 | 67.823 | |
getCellTypeReference | 10.144 | 1.857 | 12.800 | |
load_DNAmGA_Clocks_data | 32.196 | 1.184 | 37.656 | |
load_DNAm_Clocks_data | 35.439 | 1.080 | 40.273 | |
meffilEstimateCellCountsFromBetas | 13.679 | 0.259 | 14.933 | |
meffilListCellTypeReferences | 8.483 | 0.164 | 9.076 | |
plotCorClocks | 0 | 0 | 0 | |
plotDNAmAge | 40.441 | 1.321 | 46.656 | |
progress_data | 0.025 | 0.003 | 0.028 | |
progress_vars | 0.002 | 0.002 | 0.004 | |