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This page was generated on 2022-01-19 13:06:41 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 GmicR on tokay2


To the developers/maintainers of the GmicR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GmicR.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 794/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GmicR 1.8.0  (landing page)
Richard Virgen-Slane
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/GmicR
git_branch: RELEASE_3_14
git_last_commit: f795e9d
git_last_commit_date: 2021-10-26 12:54:44 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: GmicR
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GmicR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GmicR_1.8.0.tar.gz
StartedAt: 2022-01-18 20:31:11 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 21:01:19 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 1808.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GmicR.Rcheck
Warnings: 1

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:GmicR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings GmicR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GmicR.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 'GmicR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GmicR' version '1.8.0'
* 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 'GmicR' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'ape::degree' by 'bnlearn::degree' when loading 'GmicR'
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/GmicR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL-2 + file LICENSE
* 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
Namespace in Imports field not imported from: 'data.table'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GSEAGO_Builder: no visible binding for global variable 'ex'
Undefined global functions or variables:
  ex
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
GSEAGO_Builder 57.69  34.94  541.46
Auto_WGCNA     10.19   0.08   10.28
InverseARCs     6.55   0.07    6.64
bn_tabu_gen     0.07   0.00  205.28
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
GSEAGO_Builder 79.08  44.37  638.26
Auto_WGCNA     16.69   0.05   16.78
InverseARCs     7.08   0.08   10.17
bn_tabu_gen     0.11   0.02  146.10
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/GmicR.Rcheck/00check.log'
for details.



Installation output

GmicR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GmicR_1.8.0.tar.gz && rm -rf GmicR.buildbin-libdir && mkdir GmicR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GmicR.buildbin-libdir GmicR_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GmicR_1.8.0.zip && rm GmicR_1.8.0.tar.gz GmicR_1.8.0.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
 30 3576k   30 1092k    0     0  3225k      0  0:00:01 --:--:--  0:00:01 3223k
100 3576k  100 3576k    0     0  5135k      0 --:--:-- --:--:-- --:--:-- 5139k

install for i386

* installing *source* package 'GmicR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'ape::degree' by 'bnlearn::degree' when loading 'GmicR'
** help
*** installing help indices
  converting help for package 'GmicR'
    finding HTML links ... done
    Auto_WGCNA                              html  
    Batch_Net                               html  
    Data_Prep                               html  
    GO_Module_NameR                         html  
    GSEAGO_Builder                          html  
    Gmic_viz                                html  
    InverseARCs                             html  
    Query_Prep                              html  
    bn_tabu_gen                             html  
    xCell_loader                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'ape::degree' by 'bnlearn::degree' when loading 'GmicR'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'ape::degree' by 'bnlearn::degree' when loading 'GmicR'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'GmicR' ...
not using staged install with --libs-only
** testing if installed package can be loaded
Warning: replacing previous import 'ape::degree' by 'bnlearn::degree' when loading 'GmicR'
* MD5 sums
packaged installation of 'GmicR' as GmicR_1.8.0.zip
* DONE (GmicR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'GmicR' successfully unpacked and MD5 sums checked

Tests output


Example timings

GmicR.Rcheck/examples_i386/GmicR-Ex.timings

nameusersystemelapsed
Auto_WGCNA10.19 0.0810.28
Data_Prep0.670.020.75
GO_Module_NameR0.040.000.08
GSEAGO_Builder 57.69 34.94541.46
Gmic_viz0.050.000.05
InverseARCs6.550.076.64
Query_Prep0.210.000.22
bn_tabu_gen 0.07 0.00205.28
xCell_loader0.030.000.03

GmicR.Rcheck/examples_x64/GmicR-Ex.timings

nameusersystemelapsed
Auto_WGCNA16.69 0.0516.78
Data_Prep0.420.000.45
GO_Module_NameR0.030.000.03
GSEAGO_Builder 79.08 44.37638.26
Gmic_viz0.020.000.02
InverseARCs 7.08 0.0810.17
Query_Prep0.280.000.28
bn_tabu_gen 0.11 0.02146.10
xCell_loader0.040.000.29