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CHECK report for RBM on riesling1

This page was generated on 2020-10-28 13:32:13 -0400 (Wed, 28 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE RBM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1460/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RBM 1.22.0
Dongmei Li
Snapshot Date: 2020-10-27 13:12:07 -0400 (Tue, 27 Oct 2020)
URL: https://git.bioconductor.org/packages/RBM
Branch: RELEASE_3_12
Last Commit: f15d3de
Last Changed Date: 2020-10-27 11:04:01 -0400 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK YES, new version is higher than in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK YES, new version is higher than in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK YES, new version is higher than in internal repository

Summary

Package: RBM
Version: 1.22.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RBM.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RBM_1.22.0.tar.gz
StartedAt: 2020-10-27 22:06:04 -0400 (Tue, 27 Oct 2020)
EndedAt: 2020-10-27 22:07:14 -0400 (Tue, 27 Oct 2020)
EllapsedTime: 70.1 seconds
RetCode: 0
Status:  OK  
CheckDir: RBM.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RBM.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RBM_1.22.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/RBM.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RBM/DESCRIPTION' ... OK
* this is package 'RBM' version '1.22.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'RBM' 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
RBM_F: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  model.matrix
Consider adding
  importFrom("stats", "model.matrix")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
RBM-package 5.16   0.02    5.18
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
RBM-package 5.19   0.02    5.21
* 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-3.12-bioc/meat/RBM.Rcheck/00check.log'
for details.



Installation output

RBM.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/RBM_1.22.0.tar.gz && rm -rf RBM.buildbin-libdir && mkdir RBM.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RBM.buildbin-libdir RBM_1.22.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL RBM_1.22.0.zip && rm RBM_1.22.0.tar.gz RBM_1.22.0.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  170k  100  170k    0     0  1509k      0 --:--:-- --:--:-- --:--:-- 1509k

install for i386

* installing *source* package 'RBM' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RBM'
    finding HTML links ... done
    RBM-package                             html  
    RBM_F                                   html  
    RBM_T                                   html  
    ovarian_cancer_methylation              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 'RBM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RBM' as RBM_1.22.0.zip
* DONE (RBM)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'RBM' successfully unpacked and MD5 sums checked

Tests output


Example timings

RBM.Rcheck/examples_i386/RBM-Ex.timings

nameusersystemelapsed
RBM-package5.160.025.18
RBM_F4.50.04.5
RBM_T0.520.000.51

RBM.Rcheck/examples_x64/RBM-Ex.timings

nameusersystemelapsed
RBM-package5.190.025.21
RBM_F4.610.004.61
RBM_T0.530.000.53