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CHECK report for TSCAN on tokay2

This page was generated on 2020-10-17 11:57:58 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE TSCAN PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1841/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TSCAN 1.26.0
Zhicheng Ji
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/TSCAN
Branch: RELEASE_3_11
Last Commit: d2db3b0
Last Changed Date: 2020-04-27 14:42:58 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TSCAN
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TSCAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TSCAN_1.26.0.tar.gz
StartedAt: 2020-10-17 09:04:11 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 09:07:03 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 172.2 seconds
RetCode: 0
Status:  OK  
CheckDir: TSCAN.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TSCAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TSCAN_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/TSCAN.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 'TSCAN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TSCAN' version '1.26.0'
* 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 'TSCAN' 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
difftest : <anonymous>: no visible global function definition for
  'pchisq'
difftest: no visible global function definition for 'p.adjust'
exprmclust: no visible global function definition for 'prcomp'
exprmclust : <anonymous>: no visible global function definition for
  'lm'
exprmclust: no visible global function definition for 'dist'
plotmclust: no visible binding for global variable 'pca_dim_1'
plotmclust: no visible binding for global variable 'pca_dim_2'
plotmclust: no visible binding for global variable 'sample_name'
preprocess: no visible binding for global variable 'sd'
preprocess: no visible global function definition for 'hclust'
preprocess: no visible global function definition for 'dist'
preprocess: no visible global function definition for 'cutree'
preprocess: no visible global function definition for 'aggregate'
singlegeneplot: no visible global function definition for
  'fitted.values'
singlegeneplot: no visible binding for global variable 'predict'
Undefined global functions or variables:
  aggregate cutree dist fitted.values hclust lm p.adjust pca_dim_1
  pca_dim_2 pchisq prcomp predict sample_name sd
Consider adding
  importFrom("stats", "aggregate", "cutree", "dist", "fitted.values",
             "hclust", "lm", "p.adjust", "pchisq", "prcomp", "predict",
             "sd")
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
difftest 7.64   0.13    7.83
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
difftest 7.77   0.11    7.98
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/TSCAN.Rcheck/00check.log'
for details.



Installation output

TSCAN.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/TSCAN_1.26.0.tar.gz && rm -rf TSCAN.buildbin-libdir && mkdir TSCAN.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TSCAN.buildbin-libdir TSCAN_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL TSCAN_1.26.0.zip && rm TSCAN_1.26.0.tar.gz TSCAN_1.26.0.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 2560k  100 2560k    0     0  24.0M      0 --:--:-- --:--:-- --:--:-- 25.7M

install for i386

* installing *source* package 'TSCAN' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TSCAN'
    finding HTML links ... done
    TSCAN                                   html  
    TSCANorder                              html  
    TSCANui                                 html  
    difftest                                html  
    exprmclust                              html  
    lpsdata                                 html  
    orderscore                              html  
    plotmclust                              html  
    preprocess                              html  
    singlegeneplot                          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 'TSCAN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TSCAN' as TSCAN_1.26.0.zip
* DONE (TSCAN)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'TSCAN' successfully unpacked and MD5 sums checked

Tests output


Example timings

TSCAN.Rcheck/examples_i386/TSCAN-Ex.timings

nameusersystemelapsed
TSCANorder1.430.171.61
TSCANui000
difftest7.640.137.83
exprmclust1.910.142.04
orderscore2.000.092.39
plotmclust2.460.024.33
preprocess1.590.061.83
singlegeneplot2.100.032.33

TSCAN.Rcheck/examples_x64/TSCAN-Ex.timings

nameusersystemelapsed
TSCANorder2.690.053.06
TSCANui000
difftest7.770.117.98
exprmclust1.530.061.60
orderscore1.310.051.36
plotmclust1.360.051.40
preprocess1.060.031.10
singlegeneplot1.880.052.20