Dolors Pelegri-Siso
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/methylclock |
| git_branch: master |
| git_last_commit: 1856a52 |
| git_last_commit_date: 2021-11-21 05:56:37 -0400 (Sun, 21 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:00 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? 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 1124/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methylclock 1.1.2 (landing page) Dolors Pelegri-Siso
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | 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: 1.1.2 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylclock.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings methylclock_1.1.2.tar.gz |
| StartedAt: 2022-03-17 19:32:58 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:40:50 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 471.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: methylclock.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:methylclock.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings methylclock_1.1.2.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/methylclock.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methylclock/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methylclock' version '1.1.2'
* 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 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/methylclock/libs/x64/methylclock.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
commonClockCpgs 20.80 1.90 30.04
plotDNAmAge 17.60 1.19 23.65
DNAmAge 14.06 2.48 21.73
checkClocks 13.91 1.14 20.13
load_DNAm_Clocks_data 13.61 1.08 18.97
load_DNAmGA_Clocks_data 11.59 1.05 16.81
checkClocksGA 9.95 0.89 13.78
DNAmGA 7.75 0.68 11.71
meffilEstimateCellCountsFromBetas 6.47 0.37 8.08
getCellTypeReference 4.34 1.33 6.30
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/methylclock.Rcheck/00check.log'
for details.
methylclock.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL methylclock
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'methylclock' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c NewModel1Clean.cpp -o NewModel1Clean.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c NewModel1Clean_emxAPI.cpp -o NewModel1Clean_emxAPI.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c NewModel1Clean_emxutil.cpp -o NewModel1Clean_emxutil.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c NewModel1Clean_initialize.cpp -o NewModel1Clean_initialize.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c NewModel1Clean_terminate.cpp -o NewModel1Clean_terminate.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c bsxfun.cpp -o bsxfun.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c main.cpp -o main.o
main.cpp:37:14: warning: 'float argInit_real_T()' defined but not used [-Wunused-function]
static float argInit_real_T()
^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c repmat.cpp -o repmat.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c rtGetInf.cpp -o rtGetInf.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c rtGetNaN.cpp -o rtGetNaN.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c rt_nonfinite.cpp -o rt_nonfinite.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o methylclock.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-methylclock/00new/methylclock/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'methylclock'
finding HTML links ... done
DNAmAge html
DNAmGA html
checkClocks html
checkClocksGA html
commonClockCpgs html
getCellTypeReference html
load_DNAmGA_Clocks_data html
load_DNAm_Clocks_data html
meffilEstimateCellCountsFromBetas html
meffilListCellTypeReferences html
methylclock html
plotCorClocks html
plotDNAmAge html
progress_data html
progress_vars html
** 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 (methylclock)
Making 'packages.html' ... done
methylclock.Rcheck/methylclock-Ex.timings
| name | user | system | elapsed | |
| DNAmAge | 14.06 | 2.48 | 21.73 | |
| DNAmGA | 7.75 | 0.68 | 11.71 | |
| checkClocks | 13.91 | 1.14 | 20.13 | |
| checkClocksGA | 9.95 | 0.89 | 13.78 | |
| commonClockCpgs | 20.80 | 1.90 | 30.04 | |
| getCellTypeReference | 4.34 | 1.33 | 6.30 | |
| load_DNAmGA_Clocks_data | 11.59 | 1.05 | 16.81 | |
| load_DNAm_Clocks_data | 13.61 | 1.08 | 18.97 | |
| meffilEstimateCellCountsFromBetas | 6.47 | 0.37 | 8.08 | |
| meffilListCellTypeReferences | 3.53 | 0.25 | 4.37 | |
| plotCorClocks | 0 | 0 | 0 | |
| plotDNAmAge | 17.60 | 1.19 | 23.65 | |
| progress_data | 0.02 | 0.00 | 0.01 | |
| progress_vars | 0.00 | 0.02 | 0.02 | |