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This page was generated on 2022-01-24 13:07:02 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for SLGI on tokay2


To the developers/maintainers of the SLGI package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SLGI.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 1817/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SLGI 1.54.0  (landing page)
Nolwenn Le Meur
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/SLGI
git_branch: RELEASE_3_14
git_last_commit: b4f5841
git_last_commit_date: 2021-10-26 11:51:49 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: SLGI
Version: 1.54.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SLGI.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SLGI_1.54.0.tar.gz
StartedAt: 2022-01-24 02:39:42 -0500 (Mon, 24 Jan 2022)
EndedAt: 2022-01-24 02:44:51 -0500 (Mon, 24 Jan 2022)
EllapsedTime: 309.1 seconds
RetCode: 0
Status:   OK  
CheckDir: SLGI.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SLGI.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SLGI_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SLGI.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SLGI/DESCRIPTION' ... OK
* this is package 'SLGI' version '1.54.0'
* 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 'SLGI' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data      4.2Mb
    extdata  11.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'ScISI' 'lattice' 'GO.db'
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' call to 'GO.db' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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
iSummary       12.17   1.39   13.71
compare         6.92   1.87    8.80
plot            6.72   0.01    6.74
siResult-class  6.64   0.04    6.69
modelSLGI       6.51   0.04    6.57
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
iSummary       13.09   1.17   14.27
compare         6.84   0.90    7.79
siResult-class  6.28   0.01    6.29
plot            5.80   0.04    5.83
modelSLGI       5.81   0.00    5.81
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/SLGI.Rcheck/00check.log'
for details.



Installation output

SLGI.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SLGI_1.54.0.tar.gz && rm -rf SLGI.buildbin-libdir && mkdir SLGI.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SLGI.buildbin-libdir SLGI_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SLGI_1.54.0.zip && rm SLGI_1.54.0.tar.gz SLGI_1.54.0.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
  3 8105k    3  293k    0     0   986k      0  0:00:08 --:--:--  0:00:08  986k
100 8105k  100 8105k    0     0  7341k      0  0:00:01  0:00:01 --:--:-- 7348k

install for i386

* installing *source* package 'SLGI' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'BiocGenerics' for request: 'plot' when loading 'SLGI'
** help
*** installing help indices
  converting help for package 'SLGI'
    finding HTML links ... done
    Atong                                   html  
    AtongFnDomain                           html  
    AtongPair                               html  
    Boeke                                   html  
    SDL                                     html  
    SGA                                     html  
    SGD.SL                                  html  
    TFmat                                   html  
    byComplex                               html  
    comemberIn                              html  
    compare                                 html  
    congruence                              html  
    createSquareMatrix                      html  
    dSLAM.GPL1444                           html  
    domainDist                              html  
    essglist                                html  
    getInteraction                          html  
    getSharedDomains                        html  
    getSharedInteraction                    html  
    getTestedPairs                          html  
    getUniquePairs                          html  
    gi2005                                  html  
    gi2007                                  html  
    gi2Interactome                          html  
    hyperG                                  html  
    iSummary                                html  
    modelSLGI                               html  
    normInteraction                         html  
    plot                                    html  
    seqMatcherAlign                         html  
    sharedBy                                html  
    sharedInt                               html  
    siResult-class                          html  
    test2Interact                           html  
    topInteraction                          html  
    twoWayTable                             html  
    withinComplex                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'BiocGenerics' for request: 'plot' when loading 'SLGI'
** testing if installed package can be loaded from final location
No methods found in package 'BiocGenerics' for request: 'plot' when loading 'SLGI'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'SLGI' ...
** testing if installed package can be loaded
No methods found in package 'BiocGenerics' for request: 'plot' when loading 'SLGI'
* MD5 sums
packaged installation of 'SLGI' as SLGI_1.54.0.zip
* DONE (SLGI)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'SLGI' successfully unpacked and MD5 sums checked

Tests output


Example timings

SLGI.Rcheck/examples_i386/SLGI-Ex.timings

nameusersystemelapsed
Atong0.000.010.02
AtongFnDomain2.820.132.94
AtongPair0.060.010.07
SDL000
SGA0.000.020.02
SGD.SL0.150.010.17
TFmat0.10.00.1
byComplex0.750.020.76
comemberIn0.50.00.5
compare6.921.878.80
congruence0.020.000.01
createSquareMatrix0.040.020.07
domainDist1.920.051.97
essglist0.000.010.01
getInteraction000
getSharedDomains0.020.000.02
getSharedInteraction000
getTestedPairs0.000.020.01
getUniquePairs000
gi20050.030.030.06
gi20070.130.020.15
gi2Interactome000
hyperG000
iSummary12.17 1.3913.71
modelSLGI6.510.046.57
normInteraction2.570.022.57
plot6.720.016.74
seqMatcherAlign000
sharedBy2.310.042.34
sharedInt000
siResult-class6.640.046.69
test2Interact0.010.000.02
topInteraction3.770.033.79
twoWayTable3.220.033.25
withinComplex0.300.040.33

SLGI.Rcheck/examples_x64/SLGI-Ex.timings

nameusersystemelapsed
Atong0.020.020.03
AtongFnDomain3.340.063.41
AtongPair0.070.010.08
SDL000
SGA0.010.000.01
SGD.SL0.130.020.14
TFmat0.070.000.08
byComplex0.830.010.85
comemberIn0.160.040.18
compare6.840.907.79
congruence000
createSquareMatrix0.030.030.06
domainDist2.310.072.38
essglist0.000.010.01
getInteraction000
getSharedDomains0.020.000.02
getSharedInteraction000
getTestedPairs0.010.000.02
getUniquePairs0.020.000.01
gi20050.260.020.28
gi20070.180.000.17
gi2Interactome000
hyperG000
iSummary13.09 1.1714.27
modelSLGI5.810.005.81
normInteraction2.770.012.78
plot5.800.045.83
seqMatcherAlign000
sharedBy2.070.002.08
sharedInt000
siResult-class6.280.016.29
test2Interact000
topInteraction3.610.053.66
twoWayTable2.910.012.92
withinComplex0.790.000.80