| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:05:35 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 1119/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methylclock 1.0.1 (landing page) Dolors Pelegri-Siso
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: methylclock |
| Version: 1.0.1 |
| Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:methylclock.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings methylclock_1.0.1.tar.gz |
| StartedAt: 2022-04-12 08:10:32 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 08:20:08 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 576.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methylclock.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:methylclock.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings methylclock_1.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/methylclock.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.1’
* 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 ... OK
* 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’
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’
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’
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’
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.. age clock coefBohlin coefHannum
coefHorvath coefKnightGA coefLeeGA coefLevine coefMayneGA coefPedBE
coefSkin coefTL coefWu method
* 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 43.325 3.317 51.528
plotDNAmAge 31.631 2.594 37.169
DNAmAge 30.811 3.011 37.274
checkClocks 30.680 2.753 36.732
load_DNAmGA_Clocks_data 26.628 2.449 31.709
load_DNAm_Clocks_data 25.572 2.388 30.453
DNAmGA 19.948 1.656 23.592
checkClocksGA 17.764 1.404 21.125
meffilEstimateCellCountsFromBetas 9.928 0.721 11.350
getCellTypeReference 7.145 0.912 8.532
meffilListCellTypeReferences 6.361 0.400 7.151
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.14-bioc/meat/methylclock.Rcheck/00check.log’
for details.
methylclock.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL methylclock
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘methylclock’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c NewModel1Clean.cpp -o NewModel1Clean.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c NewModel1Clean_emxAPI.cpp -o NewModel1Clean_emxAPI.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c NewModel1Clean_emxutil.cpp -o NewModel1Clean_emxutil.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c NewModel1Clean_initialize.cpp -o NewModel1Clean_initialize.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c NewModel1Clean_terminate.cpp -o NewModel1Clean_terminate.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c bsxfun.cpp -o bsxfun.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c main.cpp -o main.o
main.cpp:37:14: warning: ‘float argInit_real_T()’ defined but not used [-Wunused-function]
37 | static float argInit_real_T()
| ^~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c repmat.cpp -o repmat.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c rtGetInf.cpp -o rtGetInf.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c rtGetNaN.cpp -o rtGetNaN.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c rt_nonfinite.cpp -o rt_nonfinite.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/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 -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/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 | 30.811 | 3.011 | 37.274 | |
| DNAmGA | 19.948 | 1.656 | 23.592 | |
| checkClocks | 30.680 | 2.753 | 36.732 | |
| checkClocksGA | 17.764 | 1.404 | 21.125 | |
| commonClockCpgs | 43.325 | 3.317 | 51.528 | |
| getCellTypeReference | 7.145 | 0.912 | 8.532 | |
| load_DNAmGA_Clocks_data | 26.628 | 2.449 | 31.709 | |
| load_DNAm_Clocks_data | 25.572 | 2.388 | 30.453 | |
| meffilEstimateCellCountsFromBetas | 9.928 | 0.721 | 11.350 | |
| meffilListCellTypeReferences | 6.361 | 0.400 | 7.151 | |
| plotCorClocks | 0 | 0 | 0 | |
| plotDNAmAge | 31.631 | 2.594 | 37.169 | |
| progress_data | 0.013 | 0.005 | 0.017 | |
| progress_vars | 0.000 | 0.001 | 0.001 | |