Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:25 -0400 (Fri, 15 Oct 2021).

CHECK results for TOAST on tokay2

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raw results

Package 1931/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TOAST 1.6.0  (landing page)
Ziyi Li
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/TOAST
git_branch: RELEASE_3_13
git_last_commit: 68b0442
git_last_commit_date: 2021-05-19 12:44:26 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: TOAST
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TOAST.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TOAST_1.6.0.tar.gz
StartedAt: 2021-10-15 06:43:41 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 06:48:21 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 280.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: TOAST.Rcheck
Warnings: 1

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:TOAST.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TOAST_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/TOAST.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 'TOAST/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TOAST' version '1.6.0'
* 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 'TOAST' 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 ... WARNING
Invalid citation information in 'inst/CITATION':
  Error in bibentry(bibtype = entry, textVersion = textVersion, header = header,     footer = footer, ...): object 'X' not found
* 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 ... OK
* 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
csDeconv 52.09   1.08   53.17
Tsisal    7.03   0.26    7.33
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
csDeconv 41.39   1.14   42.53
* 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 WARNING
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/TOAST.Rcheck/00check.log'
for details.



Installation output

TOAST.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/TOAST_1.6.0.tar.gz && rm -rf TOAST.buildbin-libdir && mkdir TOAST.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TOAST.buildbin-libdir TOAST_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL TOAST_1.6.0.zip && rm TOAST_1.6.0.tar.gz TOAST_1.6.0.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
 47 2922k   47 1380k    0     0  1447k      0  0:00:02 --:--:--  0:00:02 1448k
100 2922k  100 2922k    0     0  1785k      0  0:00:01  0:00:01 --:--:-- 1787k

install for i386

* installing *source* package 'TOAST' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TOAST'
    finding HTML links ... done
    CBS_PBMC_array                          html  
    ChooseMarker                            html  
    DEVarSelect                             html  
    GetPrior                                html  
    MDeconv                                 html  
    RA_100samples                           html  
    Tsisal                                  html  
    assignCellType                          html  
    beta_emp                                html  
    csDeconv                                html  
    csTest                                  html  
    findRefinx                              html  
    fitModel                                html  
    makeDesign                              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 'TOAST' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TOAST' as TOAST_1.6.0.zip
* DONE (TOAST)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'TOAST' successfully unpacked and MD5 sums checked

Tests output


Example timings

TOAST.Rcheck/examples_i386/TOAST-Ex.timings

nameusersystemelapsed
CBS_PBMC_array0.020.000.01
ChooseMarker0.070.020.08
DEVarSelect0.050.000.05
GetPrior000
MDeconv0.050.000.05
RA_100samples0.250.000.25
Tsisal7.030.267.33
assignCellType000
beta_emp0.020.000.02
csDeconv52.09 1.0853.17
csTest0.140.000.14
findRefinx0.020.000.02
fitModel0.060.000.06
makeDesign000

TOAST.Rcheck/examples_x64/TOAST-Ex.timings

nameusersystemelapsed
CBS_PBMC_array0.010.000.02
ChooseMarker0.050.000.05
DEVarSelect0.450.010.47
GetPrior000
MDeconv0.040.000.03
RA_100samples0.150.020.17
Tsisal4.860.094.95
assignCellType000
beta_emp0.020.000.02
csDeconv41.39 1.1442.53
csTest0.110.000.11
findRefinx0.010.000.01
fitModel0.070.000.07
makeDesign000