Ken Shun Hang Yip
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/Linnorm |
| Branch: RELEASE_3_12 |
| Last Commit: 5004ac6 |
| Last Changed Date: 2020-10-27 11:13:29 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:57 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the Linnorm package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 960/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Linnorm 2.14.0 (landing page) Ken Shun Hang Yip
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Linnorm |
| Version: 2.14.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Linnorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Linnorm_2.14.0.tar.gz |
| StartedAt: 2021-05-06 04:08:02 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 04:23:36 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 934.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Linnorm.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Linnorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Linnorm_2.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/Linnorm.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Linnorm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Linnorm' version '2.14.0'
* 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 whether package 'Linnorm' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Linnorm.HClust: no visible binding for global variable 'x'
Linnorm.HClust: no visible binding for global variable 'y'
Linnorm.HClust: no visible binding for global variable 'xend'
Linnorm.HClust: no visible binding for global variable 'yend'
Linnorm.HClust: no visible binding for global variable 'cluster'
Linnorm.HClust: no visible binding for global variable 'X1'
Linnorm.HClust: no visible binding for global variable 'X2'
Linnorm.HVar: no visible binding for global variable 'SD'
Linnorm.HVar: no visible binding for global variable 'group'
Undefined global functions or variables:
SD X1 X2 cluster group x xend y yend
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Linnorm/libs/i386/Linnorm.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Linnorm/libs/x64/Linnorm.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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
RnaXSim 95.90 0.20 96.18
Linnorm.Cor 85.50 0.34 88.55
Linnorm.limma 55.00 0.04 55.29
Linnorm.Norm 53.75 0.08 53.83
Linnorm 53.40 0.03 53.45
Linnorm.tSNE 6.32 0.19 6.50
Linnorm.PCA 5.65 0.39 8.72
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
RnaXSim 113.61 0.12 114.05
Linnorm.Cor 64.57 0.35 64.93
Linnorm.limma 50.19 0.02 50.20
Linnorm 48.76 0.02 48.88
Linnorm.Norm 47.65 0.01 47.67
Linnorm.tSNE 5.81 0.23 6.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* 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
'C:/Users/biocbuild/bbs-3.12-bioc/meat/Linnorm.Rcheck/00check.log'
for details.
Linnorm.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/Linnorm_2.14.0.tar.gz && rm -rf Linnorm.buildbin-libdir && mkdir Linnorm.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Linnorm.buildbin-libdir Linnorm_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL Linnorm_2.14.0.zip && rm Linnorm_2.14.0.tar.gz Linnorm_2.14.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2418k 100 2418k 0 0 22.9M 0 --:--:-- --:--:-- --:--:-- 23.1M
install for i386
* installing *source* package 'Linnorm' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Misc.cpp -o Misc.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Linnorm.dll tmp.def Misc.o -std=c++11 -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -DARMA_64BIT_WORD=1 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/Linnorm.buildbin-libdir/00LOCK-Linnorm/00new/Linnorm/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Linnorm'
finding HTML links ... done
Islam2011 html
LIHC html
LinearRegression html
LinearRegressionFP html
Linnorm.Cor html
Linnorm.DataImput html
Linnorm.HClust html
Linnorm.HVar html
Linnorm.Norm html
Linnorm.PCA html
Linnorm html
Linnorm.SGenes html
Linnorm.limma html
Linnorm.tSNE html
RnaXSim html
SEQC 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
install for x64
* installing *source* package 'Linnorm' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Misc.cpp -o Misc.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Linnorm.dll tmp.def Misc.o -std=c++11 -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -DARMA_64BIT_WORD=1 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/Linnorm.buildbin-libdir/Linnorm/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Linnorm' as Linnorm_2.14.0.zip
* DONE (Linnorm)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'Linnorm' successfully unpacked and MD5 sums checked
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Linnorm.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Linnorm)
>
> test_check("Linnorm")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
>
> proc.time()
user system elapsed
37.81 0.48 38.28
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Linnorm.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Linnorm)
>
> test_check("Linnorm")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
>
> proc.time()
user system elapsed
26.34 0.37 26.70
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Linnorm.Rcheck/examples_i386/Linnorm-Ex.timings
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Linnorm.Rcheck/examples_x64/Linnorm-Ex.timings
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