Back to Multiple platform build/check report for BioC 3.16
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-06-30 11:06:16 -0400 (Thu, 30 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4147
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4159
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 condiments on palomino4


To the developers/maintainers of the condiments package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/condiments.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 391/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
condiments 1.5.0  (landing page)
Hector Roux de Bezieux
Snapshot Date: 2022-06-29 14:00:05 -0400 (Wed, 29 Jun 2022)
git_url: https://git.bioconductor.org/packages/condiments
git_branch: master
git_last_commit: da9c063
git_last_commit_date: 2022-04-26 12:14:20 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'slingshot' which is not available

Summary

Package: condiments
Version: 1.5.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:condiments.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings condiments_1.5.0.tar.gz
StartedAt: 2022-06-30 00:30:17 -0400 (Thu, 30 Jun 2022)
EndedAt: 2022-06-30 00:39:43 -0400 (Thu, 30 Jun 2022)
EllapsedTime: 566.3 seconds
RetCode: 0
Status:   OK  
CheckDir: condiments.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:condiments.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings condiments_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/condiments.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'condiments/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'condiments' version '1.5.0'
* 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 'condiments' 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
* 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
.condition_sling: no visible binding for global variable '.'
.condition_sling : <anonymous>: no visible binding for global variable
  '.'
.distinct_inputs: no visible binding for global variable 'Samples'
.distinct_inputs: no visible binding for global variable '.'
.fateSelectionTest: no visible binding for global variable 'pair'
.fateSelectionTest: no visible binding for global variable 'statistic'
.fateSelectionTest: no visible binding for global variable 'p.value'
.multiple_samples: no visible binding for global variable 'p.value'
.progressionTest: no visible binding for global variable 'lineage'
.progressionTest: no visible binding for global variable 'statistic'
.progressionTest: no visible binding for global variable 'p.value'
.topologyTest_multipleSamples: no visible binding for global variable
  'p.value'
fateSelectionTest_multipleSamples,SlingshotDataSet: no visible binding
  for global variable 'condition'
progressionTest_multipleSamples,SlingshotDataSet: no visible binding
  for global variable 'condition'
Undefined global functions or variables:
  . Samples condition lineage p.value pair statistic
* 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 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 NOTE
See
  'F:/biocbuild/bbs-3.16-bioc/meat/condiments.Rcheck/00check.log'
for details.



Installation output

condiments.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/condiments_1.5.0.tar.gz && rm -rf condiments.buildbin-libdir && mkdir condiments.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=condiments.buildbin-libdir condiments_1.5.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL condiments_1.5.0.zip && rm condiments_1.5.0.tar.gz condiments_1.5.0.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
 15  290k   15 46557    0     0   786k      0 --:--:-- --:--:-- --:--:--  783k
100  290k  100  290k    0     0  1940k      0 --:--:-- --:--:-- --:--:-- 1939k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'condiments' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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
* MD5 sums
packaged installation of 'condiments' as condiments_1.5.0.zip
* DONE (condiments)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'condiments' successfully unpacked and MD5 sums checked

Tests output

condiments.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(condiments)
> library(testthat)
> test_check("condiments")
note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 2 unique complexity parameters in default grid. Truncating the grid to 2 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 2 unique complexity parameters in default grid. Truncating the grid to 2 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 122 ]
> 
> proc.time()
   user  system elapsed 
 266.35   62.29  330.85 

Example timings

condiments.Rcheck/condiments-Ex.timings

nameusersystemelapsed
create_differential_topology000
differentiationTest2.860.092.95
fateSelectionTest2.840.243.08
fateSelectionTest_multipleSamples4.280.034.33
imbalance_score0.220.010.23
merge_sds0.230.020.25
nLineages0.190.010.20
progressionTest0.280.000.30
progressionTest_multipleSamples0.280.020.30
slingshot_conditions0.640.010.69
topologyTest4.070.054.14
topologyTest_multipleSamples4.150.034.18
weights_from_pst0.210.020.22