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This page was generated on 2021-07-30 12:05:04 -0400 (Fri, 30 Jul 2021).

CHECK results for LOBSTAHS on riesling1

To the developers/maintainers of the LOBSTAHS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LOBSTAHS.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 979/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LOBSTAHS 1.19.0  (landing page)
James Collins
Snapshot Date: 2021-07-29 14:50:07 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/LOBSTAHS
Branch: master
Last Commit: 3deb41f
Last Changed Date: 2021-05-19 12:21:39 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  NO, package depends on 'xcms' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: LOBSTAHS
Version: 1.19.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LOBSTAHS.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings LOBSTAHS_1.19.0.tar.gz
StartedAt: 2021-07-30 01:04:49 -0400 (Fri, 30 Jul 2021)
EndedAt: 2021-07-30 01:11:58 -0400 (Fri, 30 Jul 2021)
EllapsedTime: 428.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: LOBSTAHS.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LOBSTAHS.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings LOBSTAHS_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/LOBSTAHS.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '1.19.0'
* 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:
  Warning: multiple methods tables found for 'bin'
  Warning: multiple methods tables found for 'polarity<-'
See 'D:/biocbuild/bbs-3.14-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    622Kb       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 8.66   0.12     8.8
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
loadLOBdbase  6.5   0.06    6.56
* 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
  'D:/biocbuild/bbs-3.14-bioc/meat/LOBSTAHS.Rcheck/00check.log'
for details.



Installation output

LOBSTAHS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/LOBSTAHS_1.19.0.tar.gz && rm -rf LOBSTAHS.buildbin-libdir && mkdir LOBSTAHS.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LOBSTAHS.buildbin-libdir LOBSTAHS_1.19.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL LOBSTAHS_1.19.0.zip && rm LOBSTAHS_1.19.0.tar.gz LOBSTAHS_1.19.0.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
 56 2701k   56 1517k    0     0  2789k      0 --:--:-- --:--:-- --:--:-- 2784k
100 2701k  100 2701k    0     0  3049k      0 --:--:-- --:--:-- --:--:-- 3045k

install for i386

* installing *source* package 'LOBSTAHS' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
multiple methods tables found for 'bin' 
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  
REDIRECT:topic	 LOBisoID_diagnostics<-,LOBSet-method -> LOBSet-class.html [ FAIL ]
REDIRECT:topic	 LOBisoID_diagnostics<- -> LOBSet-class.html [ FAIL ]
REDIRECT:topic	 peakdata<-,LOBSet-method -> LOBSet-class.html [ FAIL ]
REDIRECT:topic	 peakdata<- -> LOBSet-class.html [ FAIL ]
REDIRECT:topic	 polarity<-,LOBSet-method -> LOBSet-class.html [ FAIL ]
REDIRECT:topic	 polarity<- -> LOBSet-class.html [ FAIL ]
REDIRECT:topic	 sampnames<-,LOBSet-method -> LOBSet-class.html [ FAIL ]
REDIRECT:topic	 sampnames<- -> LOBSet-class.html [ FAIL ]
REDIRECT:topic	 LOBscreen_settings<-,LOBSet-method -> LOBSet-class.html [ FAIL ]
REDIRECT:topic	 LOBscreen_settings<- -> LOBSet-class.html [ FAIL ]
REDIRECT:topic	 LOBscreen_diagnostics<-,LOBSet-method -> LOBSet-class.html [ FAIL ]
REDIRECT:topic	 LOBscreen_diagnostics<- -> LOBSet-class.html [ FAIL ]
    finding level-2 HTML links ... done

    LOBSet                                  html  
    LOBdbase-class                          html  
REDIRECT:topic	 frag_ID<-,LOBdbase-method -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 frag_ID<- -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 mz<-,LOBdbase-method -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 mz<- -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 exact_parent_neutral_mass<-,LOBdbase-method -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 exact_parent_neutral_mass<- -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 lipid_class<-,LOBdbase-method -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 lipid_class<- -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 species<-,LOBdbase-method -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 species<- -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 adduct<-,LOBdbase-method -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 adduct<- -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 adduct_rank<-,LOBdbase-method -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 adduct_rank<- -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 FA_total_no_C<-,LOBdbase-method -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 FA_total_no_C<- -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 FA_total_no_DB<-,LOBdbase-method -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 FA_total_no_DB<- -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 degree_oxidation<-,LOBdbase-method -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 degree_oxidation<- -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 parent_elem_formula<-,LOBdbase-method -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 parent_elem_formula<- -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 parent_compound_name<-,LOBdbase-method -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 parent_compound_name<- -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 polarity<-,LOBdbase-method -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 num_entries<-,LOBdbase-method -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 num_entries<- -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 num_compounds<-,LOBdbase-method -> LOBdbase-class.html [ FAIL ]
REDIRECT:topic	 num_compounds<- -> LOBdbase-class.html [ FAIL ]
    LOBdbase                                html  
    LOBdefaults                             html  
    doLOBscreen                             html  
    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: multiple methods tables found for 'bin'
Warning: multiple methods tables found for 'polarity<-'
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for 'bin'
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: multiple methods tables found for 'bin'
Warning: multiple methods tables found for 'polarity<-'
* MD5 sums
packaged installation of 'LOBSTAHS' as LOBSTAHS_1.19.0.zip
* DONE (LOBSTAHS)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'LOBSTAHS' successfully unpacked and MD5 sums checked

Tests output


Example timings

LOBSTAHS.Rcheck/examples_i386/LOBSTAHS-Ex.timings

nameusersystemelapsed
LOBSet-class0.010.000.01
LOBSet000
LOBdbase-class000
LOBdbase000
doLOBscreen2.050.082.16
exportDBtoCSV2.340.062.41
extractLOBdbasedata0.240.020.25
generateLOBdbase000
getLOBpeaklist0.010.000.01
loadLOBdbase8.660.128.80

LOBSTAHS.Rcheck/examples_x64/LOBSTAHS-Ex.timings

nameusersystemelapsed
LOBSet-class000
LOBSet000
LOBdbase-class000
LOBdbase000
doLOBscreen1.840.061.90
exportDBtoCSV2.040.042.07
extractLOBdbasedata0.210.000.21
generateLOBdbase000
getLOBpeaklist0.040.000.04
loadLOBdbase6.500.066.56