Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:10 -0400 (Fri, 15 Oct 2021).

CHECK results for M3C on tokay2

To the developers/maintainers of the M3C package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/M3C.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.

raw results

Package 1010/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3C 1.14.0  (landing page)
Christopher John
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/M3C
git_branch: RELEASE_3_13
git_last_commit: 9875790
git_last_commit_date: 2021-05-19 12:29:32 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: M3C
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:M3C.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings M3C_1.14.0.tar.gz
StartedAt: 2021-10-15 01:14:39 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 01:16:48 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 129.0 seconds
RetCode: 0
Status:   OK  
CheckDir: M3C.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:M3C.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings M3C_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/M3C.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'M3C/DESCRIPTION' ... OK
* this is package 'M3C' version '1.14.0'
* 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 'M3C' 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
CDF: no visible global function definition for 'ecdf'
CDF: no visible global function definition for 'complete.cases'
CDF: no visible binding for global variable 'consensusindex'
CDF: no visible binding for global variable 'k'
CDF: no visible binding for global variable 'K'
CDF: no visible binding for global variable 'PAC_SCORE'
M3C: no visible global function definition for 'exprs'
M3C: no visible global function definition for 'is'
M3C: no visible global function definition for 'capture.output'
M3C: no visible global function definition for 'txtProgressBar'
M3C : progress: no visible global function definition for
  'setTxtProgressBar'
M3C: no visible global function definition for 'prcomp'
M3C: no visible global function definition for 'cov'
M3C: no visible global function definition for 'rnorm'
M3C: no visible binding for global variable 'sd'
M3C: no visible binding for global variable 'var'
M3C : <anonymous>: no visible global function definition for 'pbeta'
M3C : <anonymous>: no visible global function definition for 'pnorm'
M3C: no visible binding for global variable 'K'
M3C: no visible binding for global variable 'RCSI'
M3C: no visible global function definition for 'qnorm'
M3C: no visible binding for global variable 'RCSI_SE'
M3C: no visible binding for global variable 'P_SCORE'
M3Creal: no visible global function definition for 'hclust'
M3Creal: no visible global function definition for 'as.dist'
M3Creal: no visible global function definition for 'cutree'
M3Creal: no visible global function definition for 'is'
PCSI_plot: no visible binding for global variable 'K'
PCSI_plot: no visible binding for global variable 'PCSI'
ccRun: no visible global function definition for 'dist'
ccRun: no visible global function definition for 'as.dist'
ccRun: no visible global function definition for 'kmeans'
ccRun: no visible global function definition for 'hclust'
ccRun: no visible global function definition for 'cutree'
clustersim : addnoise: no visible global function definition for
  'rnorm'
clustersim: no visible global function definition for 'rnorm'
clustersim: no visible binding for global variable 'X3'
clustersim: no visible global function definition for 'prcomp'
clustersim: no visible global function definition for 'kmeans'
clustersim: no visible binding for global variable 'PC1'
clustersim: no visible binding for global variable 'PC2'
featurefilter: no visible binding for global variable 'sd'
featurefilter: no visible global function definition for 'quantile'
featurefilter: no visible binding for global variable 'mad'
getl: no visible global function definition for 'kmeans'
getl: no visible global function definition for 'dist'
getl: no visible global function definition for 'hclust'
getl: no visible global function definition for 'cutree'
pca: no visible global function definition for 'prcomp'
pca: no visible global function definition for 'png'
pca: no visible global function definition for 'dev.off'
pca: no visible binding for global variable 'label'
rbfkernel: no visible global function definition for 'dist'
tsne: no visible binding for global variable 'X1'
tsne: no visible binding for global variable 'X2'
tsne: no visible global function definition for 'png'
tsne: no visible global function definition for 'dev.off'
tsne: no visible binding for global variable 'label'
umap: no visible binding for global variable 'X1'
umap: no visible binding for global variable 'X2'
umap: no visible global function definition for 'png'
umap: no visible global function definition for 'dev.off'
umap: no visible binding for global variable 'label'
Undefined global functions or variables:
  K PAC_SCORE PC1 PC2 PCSI P_SCORE RCSI RCSI_SE X1 X2 X3 as.dist
  capture.output complete.cases consensusindex cov cutree dev.off dist
  ecdf exprs hclust is k kmeans label mad pbeta png pnorm prcomp qnorm
  quantile rnorm sd setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "complete.cases", "cov", "cutree",
             "dist", "ecdf", "hclust", "kmeans", "mad", "pbeta", "pnorm",
             "prcomp", "qnorm", "quantile", "rnorm", "sd", "var")
  importFrom("utils", "capture.output", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 LazyData ... 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
M3C 1.97   0.01   24.02
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
    user system elapsed
M3C    2      0    21.5
* 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-3.13-bioc/meat/M3C.Rcheck/00check.log'
for details.



Installation output

M3C.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/M3C_1.14.0.tar.gz && rm -rf M3C.buildbin-libdir && mkdir M3C.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=M3C.buildbin-libdir M3C_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL M3C_1.14.0.zip && rm M3C_1.14.0.tar.gz M3C_1.14.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  319k  100  319k    0     0   769k      0 --:--:-- --:--:-- --:--:--  769k

install for i386

* installing *source* package 'M3C' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'M3C'
    finding HTML links ... done
    M3C                                     html  
    clustersim                              html  
    desx                                    html  
    featurefilter                           html  
    mydata                                  html  
    pca                                     html  
    tsne                                    html  
    umap                                    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 'M3C' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'M3C' as M3C_1.14.0.zip
* DONE (M3C)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'M3C' successfully unpacked and MD5 sums checked

Tests output


Example timings

M3C.Rcheck/examples_i386/M3C-Ex.timings

nameusersystemelapsed
M3C 1.97 0.0124.02
clustersim0.360.040.39
featurefilter0.210.000.22
pca0.040.000.03
tsne0.070.000.08
umap0.360.000.36

M3C.Rcheck/examples_x64/M3C-Ex.timings

nameusersystemelapsed
M3C 2.0 0.021.5
clustersim0.370.030.40
featurefilter0.240.000.24
pca0.010.010.03
tsne0.080.000.08
umap0.350.000.34