Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJK[L]MNOPQRSTUVWXYZ

CHECK report for LOBSTAHS on tokay2

This page was generated on 2020-10-17 11:56:58 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE LOBSTAHS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 947/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LOBSTAHS 1.14.0
James Collins
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/LOBSTAHS
Branch: RELEASE_3_11
Last Commit: fe67494
Last Changed Date: 2020-04-27 14:59:17 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: LOBSTAHS
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LOBSTAHS.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings LOBSTAHS_1.14.0.tar.gz
StartedAt: 2020-10-17 05:32:26 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:39:06 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 400.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: LOBSTAHS.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LOBSTAHS.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings LOBSTAHS_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/LOBSTAHS.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 'LOBSTAHS/DESCRIPTION' ... OK
* this is package 'LOBSTAHS' version '1.14.0'
* 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 'LOBSTAHS' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpA1Qe49/R.INSTALL28d85dad1e5b/LOBSTAHS/man/doLOBscreen.Rd:20: file link 'findIsotopes' in package 'CAMERA' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpA1Qe49/R.INSTALL28d85dad1e5b/LOBSTAHS/man/doLOBscreen.Rd:41: file link 'findIsotopes' in package 'CAMERA' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpA1Qe49/R.INSTALL28d85dad1e5b/LOBSTAHS/man/doLOBscreen.Rd:125: file link 'findIsotopes' in package 'CAMERA' does not exist and so has been treated as a topic
  Warning: multiple methods tables found for 'polarity<-'
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/LOBSTAHS.Rcheck/00install.out' for details.
* 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 ... NOTE
Warning: multiple methods tables found for 'polarity<-'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
Warning: multiple methods tables found for 'polarity<-'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
** 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                         old_size new_size compress
  default.LOBdbase.RData    2.0Mb    621Kb       xz
* checking installed files from 'inst/doc' ... 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
loadLOBdbase 12.98   0.28   13.26
doLOBscreen   4.83   0.11    5.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
loadLOBdbase 13.52   0.09   13.62
* 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 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/LOBSTAHS.Rcheck/00check.log'
for details.



Installation output

LOBSTAHS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/LOBSTAHS_1.14.0.tar.gz && rm -rf LOBSTAHS.buildbin-libdir && mkdir LOBSTAHS.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LOBSTAHS.buildbin-libdir LOBSTAHS_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL LOBSTAHS_1.14.0.zip && rm LOBSTAHS_1.14.0.tar.gz LOBSTAHS_1.14.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2702k  100 2702k    0     0  13.6M      0 --:--:-- --:--:-- --:--:-- 14.1M

install for i386

* installing *source* package 'LOBSTAHS' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA' 
Creating a new generic function for 'polarity<-' in package 'LOBSTAHS'
** help
*** installing help indices
  converting help for package 'LOBSTAHS'
    finding HTML links ... done
    LOBSet-class                            html  
    finding level-2 HTML links ... done

    LOBSet                                  html  
    LOBdbase-class                          html  
    LOBdbase                                html  
    LOBdefaults                             html  
    doLOBscreen                             html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpA1Qe49/R.INSTALL28d85dad1e5b/LOBSTAHS/man/doLOBscreen.Rd:20: file link 'findIsotopes' in package 'CAMERA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpA1Qe49/R.INSTALL28d85dad1e5b/LOBSTAHS/man/doLOBscreen.Rd:41: file link 'findIsotopes' in package 'CAMERA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpA1Qe49/R.INSTALL28d85dad1e5b/LOBSTAHS/man/doLOBscreen.Rd:125: file link 'findIsotopes' in package 'CAMERA' does not exist and so has been treated as a topic
    exportDBtoCSV                           html  
    extractLOBdbasedata                     html  
    generateLOBdbase                        html  
    getLOBpeaklist                          html  
    loadLOBdbase                            html  
** building package indices
** installing vignettes
   'LOBSTAHS.Rmd' using 'UTF-8' 
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA'
Warning: multiple methods tables found for 'polarity<-'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA'
Warning: multiple methods tables found for 'polarity<-'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'LOBSTAHS' ...
** testing if installed package can be loaded
Warning: replacing previous import 'xcms::plot' by 'graphics::plot' when loading 'CAMERA'
Warning: multiple methods tables found for 'polarity<-'
* MD5 sums
packaged installation of 'LOBSTAHS' as LOBSTAHS_1.14.0.zip
* DONE (LOBSTAHS)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'LOBSTAHS' successfully unpacked and MD5 sums checked

Tests output


Example timings

LOBSTAHS.Rcheck/examples_i386/LOBSTAHS-Ex.timings

nameusersystemelapsed
LOBSet-class000
LOBSet000
LOBdbase-class000
LOBdbase000
doLOBscreen4.830.115.44
exportDBtoCSV4.280.104.38
extractLOBdbasedata0.340.030.37
generateLOBdbase000
getLOBpeaklist0.040.010.05
loadLOBdbase12.98 0.2813.26

LOBSTAHS.Rcheck/examples_x64/LOBSTAHS-Ex.timings

nameusersystemelapsed
LOBSet-class000
LOBSet000
LOBdbase-class000
LOBdbase000
doLOBscreen3.310.093.40
exportDBtoCSV3.370.083.47
extractLOBdbasedata0.500.030.53
generateLOBdbase000
getLOBpeaklist0.080.000.08
loadLOBdbase13.52 0.0913.62