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This page was generated on 2022-04-13 12:06:47 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (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

CHECK results for Linnorm on tokay2


To the developers/maintainers of the Linnorm package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Linnorm.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.

raw results

Package 1001/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Linnorm 2.18.0  (landing page)
Ken Shun Hang Yip
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/Linnorm
git_branch: RELEASE_3_14
git_last_commit: 2e5102d
git_last_commit_date: 2021-10-26 12:26:53 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Linnorm
Version: 2.18.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Linnorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Linnorm_2.18.0.tar.gz
StartedAt: 2022-04-12 22:00:58 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 22:14:19 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 800.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Linnorm.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Linnorm.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Linnorm_2.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Linnorm.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '2.18.0'
* 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-3.14-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-3.14-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       79.62   0.24   79.86
Linnorm.Cor   56.43   0.31   56.74
Linnorm.limma 47.07   0.01   47.08
Linnorm.Norm  46.87   0.05   46.94
Linnorm       46.53   0.03   46.56
Linnorm.tSNE   6.17   0.11    6.41
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
RnaXSim       94.83   0.06   94.90
Linnorm.Cor   52.31   0.19   52.54
Linnorm.Norm  47.28   0.04   47.31
Linnorm       46.35   0.03   46.37
Linnorm.limma 46.19   0.02   46.20
Linnorm.PCA    5.44   0.39    5.96
Linnorm.tSNE   4.95   0.09    5.07
* 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-3.14-bioc/meat/Linnorm.Rcheck/00check.log'
for details.



Installation output

Linnorm.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Linnorm_2.18.0.tar.gz && rm -rf Linnorm.buildbin-libdir && mkdir Linnorm.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Linnorm.buildbin-libdir Linnorm_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Linnorm_2.18.0.zip && rm Linnorm_2.18.0.tar.gz Linnorm_2.18.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 83 2420k   83 2018k    0     0  2556k      0 --:--:-- --:--:-- --:--:-- 2557k
100 2420k  100 2420k    0     0  2686k      0 --:--:-- --:--:-- --:--:-- 2686k

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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -DARMA_64BIT_WORD=1 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-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-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -DARMA_64BIT_WORD=1 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/Linnorm.buildbin-libdir/Linnorm/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Linnorm' as Linnorm_2.18.0.zip
* DONE (Linnorm)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Linnorm' successfully unpacked and MD5 sums checked

Tests output

Linnorm.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
  25.12    0.53   25.62 

Linnorm.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
  26.84    0.32   27.15 

Example timings

Linnorm.Rcheck/examples_i386/Linnorm-Ex.timings

nameusersystemelapsed
LinearRegression000
LinearRegressionFP000
Linnorm.Cor56.43 0.3156.74
Linnorm.DataImput2.010.142.15
Linnorm.HClust3.530.233.77
Linnorm.HVar1.320.141.45
Linnorm.Norm46.87 0.0546.94
Linnorm.PCA3.770.284.14
Linnorm46.53 0.0346.56
Linnorm.SGenes0.390.070.46
Linnorm.limma47.07 0.0147.08
Linnorm.tSNE6.170.116.41
RnaXSim79.62 0.2479.86

Linnorm.Rcheck/examples_x64/Linnorm-Ex.timings

nameusersystemelapsed
LinearRegression0.000.000.02
LinearRegressionFP000
Linnorm.Cor52.31 0.1952.54
Linnorm.DataImput2.300.172.47
Linnorm.HClust3.030.143.17
Linnorm.HVar1.060.091.16
Linnorm.Norm47.28 0.0447.31
Linnorm.PCA5.440.395.96
Linnorm46.35 0.0346.37
Linnorm.SGenes0.290.060.36
Linnorm.limma46.19 0.0246.20
Linnorm.tSNE4.950.095.07
RnaXSim94.83 0.0694.90