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CHECK report for simpIntLists on riesling1

This page was generated on 2021-01-14 15:59:11 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE simpIntLists PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 333/385HostnameOS / ArchINSTALLBUILDCHECK
simpIntLists 1.27.0
Kircicegi Korkmaz
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/simpIntLists
Branch: master
Last Commit: 4013f06
Last Changed Date: 2020-10-27 09:52:37 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ]

Summary

Package: simpIntLists
Version: 1.27.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:simpIntLists.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings simpIntLists_1.27.0.tar.gz
StartedAt: 2021-01-14 11:41:58 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:43:02 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 64.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: simpIntLists.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:simpIntLists.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings simpIntLists_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/simpIntLists.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'simpIntLists/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'simpIntLists' version '1.27.0'
* 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 'simpIntLists' 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
findInteractionList: no visible global function definition for 'data'
findInteractionList: no visible binding for global variable
  'ArabidopsisBioGRIDInteractionEntrezId'
findInteractionList: no visible binding for global variable
  'ArabidopsisBioGRIDInteractionOfficial'
findInteractionList: no visible binding for global variable
  'ArabidopsisBioGRIDInteractionUniqueId'
findInteractionList: no visible binding for global variable
  'C.elegansBioGRIDInteractionEntrezId'
findInteractionList: no visible binding for global variable
  'C.elegansBioGRIDInteractionOfficial'
findInteractionList: no visible binding for global variable
  'C.elegansBioGRIDInteractionUniqueId'
findInteractionList: no visible binding for global variable
  'FruitFlyBioGRIDInteractionEntrezId'
findInteractionList: no visible binding for global variable
  'FruitFlyBioGRIDInteractionOfficial'
findInteractionList: no visible binding for global variable
  'FruitFlyBioGRIDInteractionUniqueId'
findInteractionList: no visible binding for global variable
  'HumanBioGRIDInteractionEntrezId'
findInteractionList: no visible binding for global variable
  'HumanBioGRIDInteractionOfficial'
findInteractionList: no visible binding for global variable
  'HumanBioGRIDInteractionUniqueId'
findInteractionList: no visible binding for global variable
  'MouseBioGRIDInteractionEntrezId'
findInteractionList: no visible binding for global variable
  'MouseBioGRIDInteractionOfficial'
findInteractionList: no visible binding for global variable
  'MouseBioGRIDInteractionUniqueId'
findInteractionList: no visible binding for global variable
  'YeastBioGRIDInteractionEntrezId'
findInteractionList: no visible binding for global variable
  'YeastBioGRIDInteractionOfficial'
findInteractionList: no visible binding for global variable
  'YeastBioGRIDInteractionUniqueId'
findInteractionList: no visible binding for global variable
  'S.pombeBioGRIDInteractionEntrezId'
findInteractionList: no visible binding for global variable
  'S.pombeBioGRIDInteractionOfficial'
findInteractionList: no visible binding for global variable
  'S.pombeBioGRIDInteractionUniqueId'
Undefined global functions or variables:
  ArabidopsisBioGRIDInteractionEntrezId
  ArabidopsisBioGRIDInteractionOfficial
  ArabidopsisBioGRIDInteractionUniqueId
  C.elegansBioGRIDInteractionEntrezId
  C.elegansBioGRIDInteractionOfficial
  C.elegansBioGRIDInteractionUniqueId
  FruitFlyBioGRIDInteractionEntrezId FruitFlyBioGRIDInteractionOfficial
  FruitFlyBioGRIDInteractionUniqueId HumanBioGRIDInteractionEntrezId
  HumanBioGRIDInteractionOfficial HumanBioGRIDInteractionUniqueId
  MouseBioGRIDInteractionEntrezId MouseBioGRIDInteractionOfficial
  MouseBioGRIDInteractionUniqueId S.pombeBioGRIDInteractionEntrezId
  S.pombeBioGRIDInteractionOfficial S.pombeBioGRIDInteractionUniqueId
  YeastBioGRIDInteractionEntrezId YeastBioGRIDInteractionOfficial
  YeastBioGRIDInteractionUniqueId data
Consider adding
  importFrom("utils", "data")
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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                            old_size new_size compress
  ArabidopsisBioGRIDInteractionEntrezId.rda     26Kb     19Kb    bzip2
  ArabidopsisBioGRIDInteractionOfficial.rda     34Kb     22Kb    bzip2
  ArabidopsisBioGRIDInteractionUniqueId.rda     32Kb     21Kb    bzip2
  C.ElegansBioGRIDInteractionEntrezId.rda       44Kb     32Kb    bzip2
  C.ElegansBioGRIDInteractionOfficial.rda       65Kb     38Kb    bzip2
  C.ElegansBioGRIDInteractionUniqueId.rda       64Kb     36Kb    bzip2
  FruitFlyBioGRIDInteractionEntrezId.rda       165Kb    112Kb    bzip2
  FruitFlyBioGRIDInteractionOfficial.rda       252Kb    139Kb    bzip2
  FruitFlyBioGRIDInteractionUniqueId.rda       208Kb    121Kb    bzip2
  HumanBioGRIDInteractionEntrezId.rda          222Kb    157Kb    bzip2
  HumanBioGRIDInteractionOfficial.rda          318Kb    190Kb    bzip2
  HumanBioGRIDInteractionUniqueId.rda           29Kb     18Kb    bzip2
  MouseBioGRIDInteractionEntrezId.rda           25Kb     20Kb    bzip2
  MouseBioGRIDInteractionOfficial.rda           34Kb     23Kb    bzip2
  S.PombeBioGRIDInteractionEntrezId.rda         55Kb     37Kb    bzip2
  S.PombeBioGRIDInteractionOfficial.rda         76Kb     44Kb    bzip2
  S.PombeBioGRIDInteractionUniqueId.rda         89Kb     43Kb    bzip2
  YeastBioGRIDInteractionEntrezId.rda          685Kb    469Kb    bzip2
  YeastBioGRIDInteractionOfficial.rda          958Kb    572Kb    bzip2
  YeastBioGRIDInteractionUniqueId.rda          903Kb    533Kb    bzip2
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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, 1 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/simpIntLists.Rcheck/00check.log'
for details.



Installation output

simpIntLists.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/simpIntLists_1.27.0.tar.gz && rm -rf simpIntLists.buildbin-libdir && mkdir simpIntLists.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=simpIntLists.buildbin-libdir simpIntLists_1.27.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL simpIntLists_1.27.0.zip && rm simpIntLists_1.27.0.tar.gz simpIntLists_1.27.0.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 4301k    0 14355    0     0  30607      0  0:02:23 --:--:--  0:02:23 30542
 59 4301k   59 2573k    0     0  2005k      0  0:00:02  0:00:01  0:00:01 2004k
100 4301k  100 4301k    0     0  1934k      0  0:00:02  0:00:02 --:--:-- 1934k

install for i386

* installing *source* package 'simpIntLists' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'simpIntLists'
    finding HTML links ... done
    ArabidopsisBioGRIDInteractionEntrezId   html  
REDIRECT:topic	 ArabidopsisBioGRIDInteractionEntrezId -> ArabidopsisBioGRIDInteractionEntrezId.html [ SUCCESS ]
    ArabidopsisBioGRIDInteractionOfficial   html  
REDIRECT:topic	 ArabidopsisBioGRIDInteractionOfficial -> ArabidopsisBioGRIDInteractionOfficial.html [ SUCCESS ]
    ArabidopsisBioGRIDInteractionUniqueId   html  
REDIRECT:topic	 ArabidopsisBioGRIDInteractionUniqueId -> ArabidopsisBioGRIDInteractionUniqueId.html [ SUCCESS ]
    C.ElegansBioGRIDInteractionEntrezId     html  
REDIRECT:topic	 C.ElegansBioGRIDInteractionEntrezId -> C.ElegansBioGRIDInteractionEntrezId.html [ SUCCESS ]
    C.ElegansBioGRIDInteractionOfficial     html  
REDIRECT:topic	 C.ElegansBioGRIDInteractionOfficial -> C.ElegansBioGRIDInteractionOfficial.html [ SUCCESS ]
    C.ElegansBioGRIDInteractionUniqueId     html  
REDIRECT:topic	 C.ElegansBioGRIDInteractionUniqueId -> C.ElegansBioGRIDInteractionUniqueId.html [ SUCCESS ]
    FruitFlyBioGRIDInteractionEntrezId      html  
REDIRECT:topic	 FruitFlyBioGRIDInteractionEntrezId -> FruitFlyBioGRIDInteractionEntrezId.html [ SUCCESS ]
    FruitFlyBioGRIDInteractionOfficial      html  
REDIRECT:topic	 FruitFlyBioGRIDInteractionOfficial -> FruitFlyBioGRIDInteractionOfficial.html [ SUCCESS ]
    FruitFlyBioGRIDInteractionUniqueId      html  
REDIRECT:topic	 FruitFlyBioGRIDInteractionUniqueId -> FruitFlyBioGRIDInteractionUniqueId.html [ SUCCESS ]
    HumanBioGRIDInteractionEntrezId         html  
REDIRECT:topic	 HumanBioGRIDInteractionEntrezId -> HumanBioGRIDInteractionEntrezId.html [ SUCCESS ]
    HumanBioGRIDInteractionOfficial         html  
REDIRECT:topic	 HumanBioGRIDInteractionOfficial -> HumanBioGRIDInteractionOfficial.html [ SUCCESS ]
    HumanBioGRIDInteractionUniqueId         html  
REDIRECT:topic	 HumanBioGRIDInteractionUniqueId -> HumanBioGRIDInteractionUniqueId.html [ SUCCESS ]
    MouseBioGRIDInteractionEntrezId         html  
REDIRECT:topic	 MouseBioGRIDInteractionEntrezId -> MouseBioGRIDInteractionEntrezId.html [ SUCCESS ]
    MouseBioGRIDInteractionOfficial         html  
REDIRECT:topic	 MouseBioGRIDInteractionOfficial -> MouseBioGRIDInteractionOfficial.html [ SUCCESS ]
    MouseBioGRIDInteractionUniqueId         html  
REDIRECT:topic	 MouseBioGRIDInteractionUniqueId -> MouseBioGRIDInteractionUniqueId.html [ SUCCESS ]
    S.PombeBioGRIDInteractionEntrezId       html  
REDIRECT:topic	 S.PombeBioGRIDInteractionEntrezId -> S.PombeBioGRIDInteractionEntrezId.html [ SUCCESS ]
    S.PombeBioGRIDInteractionOfficial       html  
REDIRECT:topic	 S.PombeBioGRIDInteractionOfficial -> S.PombeBioGRIDInteractionOfficial.html [ SUCCESS ]
    S.PombeBioGRIDInteractionUniqueId       html  
REDIRECT:topic	 S.PombeBioGRIDInteractionUniqueId -> S.PombeBioGRIDInteractionUniqueId.html [ SUCCESS ]
    YeastBioGRIDInteractionEntrezId         html  
REDIRECT:topic	 YeastBioGRIDInteractionEntrezId -> YeastBioGRIDInteractionEntrezId.html [ SUCCESS ]
    YeastBioGRIDInteractionOfficial         html  
REDIRECT:topic	 YeastBioGRIDInteractionOfficial -> YeastBioGRIDInteractionOfficial.html [ SUCCESS ]
    YeastBioGRIDInteractionUniqueId         html  
REDIRECT:topic	 YeastBioGRIDInteractionUniqueId -> YeastBioGRIDInteractionUniqueId.html [ SUCCESS ]
    findInteractionList                     html  
REDIRECT:topic	 findInteractionList -> findInteractionList.html [ SUCCESS ]
    simpIntLists                            html  
REDIRECT:topic	 simpIntLists-package -> simpIntLists.html [ SUCCESS ]
REDIRECT:topic	 simpIntLists -> simpIntLists.html [ SUCCESS ]
** 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 'simpIntLists' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'simpIntLists' as simpIntLists_1.27.0.zip
* DONE (simpIntLists)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'simpIntLists' successfully unpacked and MD5 sums checked

Tests output


Example timings

simpIntLists.Rcheck/examples_i386/simpIntLists-Ex.timings

nameusersystemelapsed
ArabidopsisBioGRIDInteractionEntrezId0.020.070.09
ArabidopsisBioGRIDInteractionOfficial0.060.040.10
ArabidopsisBioGRIDInteractionUniqueId0.050.040.10
C.ElegansBioGRIDInteractionEntrezId0.080.070.14
C.ElegansBioGRIDInteractionOfficial0.070.070.15
C.ElegansBioGRIDInteractionUniqueId0.070.100.16
FruitFlyBioGRIDInteractionEntrezId0.200.180.39
FruitFlyBioGRIDInteractionOfficial0.120.320.44
FruitFlyBioGRIDInteractionUniqueId0.240.220.46
HumanBioGRIDInteractionEntrezId0.220.290.51
HumanBioGRIDInteractionOfficial0.230.350.57
HumanBioGRIDInteractionUniqueId0.020.040.06
MouseBioGRIDInteractionEntrezId0.040.050.10
MouseBioGRIDInteractionOfficial0.070.030.09
MouseBioGRIDInteractionUniqueId000
S.PombeBioGRIDInteractionEntrezId0.030.100.13
S.PombeBioGRIDInteractionOfficial0.080.090.17
S.PombeBioGRIDInteractionUniqueId0.070.110.19
YeastBioGRIDInteractionEntrezId0.470.671.14
YeastBioGRIDInteractionOfficial0.850.531.37
YeastBioGRIDInteractionUniqueId0.730.721.46
findInteractionList0.030.060.09
simpIntLists0.140.050.19

simpIntLists.Rcheck/examples_x64/simpIntLists-Ex.timings

nameusersystemelapsed
ArabidopsisBioGRIDInteractionEntrezId0.000.090.09
ArabidopsisBioGRIDInteractionOfficial0.020.060.08
ArabidopsisBioGRIDInteractionUniqueId0.020.070.07
C.ElegansBioGRIDInteractionEntrezId0.040.070.12
C.ElegansBioGRIDInteractionOfficial0.070.080.15
C.ElegansBioGRIDInteractionUniqueId0.070.070.14
FruitFlyBioGRIDInteractionEntrezId0.100.260.36
FruitFlyBioGRIDInteractionOfficial0.230.170.40
FruitFlyBioGRIDInteractionUniqueId0.220.190.41
HumanBioGRIDInteractionEntrezId0.170.270.44
HumanBioGRIDInteractionOfficial0.270.250.51
HumanBioGRIDInteractionUniqueId0.030.030.06
MouseBioGRIDInteractionEntrezId0.020.060.08
MouseBioGRIDInteractionOfficial0.040.050.10
MouseBioGRIDInteractionUniqueId0.000.010.01
S.PombeBioGRIDInteractionEntrezId0.050.080.13
S.PombeBioGRIDInteractionOfficial0.090.060.16
S.PombeBioGRIDInteractionUniqueId0.090.100.19
YeastBioGRIDInteractionEntrezId0.350.721.06
YeastBioGRIDInteractionOfficial0.610.601.22
YeastBioGRIDInteractionUniqueId0.540.791.33
findInteractionList0.050.030.08
simpIntLists0.110.060.18