Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-07-08 11:57:44 -0400 (Fri, 08 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4351
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4154
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4166
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 famat on palomino4


To the developers/maintainers of the famat package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/famat.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 641/2130HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
famat 1.7.0  (landing page)
Mathieu Charles
Snapshot Date: 2022-07-07 14:00:04 -0400 (Thu, 07 Jul 2022)
git_url: https://git.bioconductor.org/packages/famat
git_branch: master
git_last_commit: 866d8a4
git_last_commit_date: 2022-04-26 12:10:11 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    ERROR    OK  

Summary

Package: famat
Version: 1.7.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:famat.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings famat_1.7.0.tar.gz
StartedAt: 2022-07-08 01:36:43 -0400 (Fri, 08 Jul 2022)
EndedAt: 2022-07-08 01:42:41 -0400 (Fri, 08 Jul 2022)
EllapsedTime: 357.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: famat.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:famat.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings famat_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/famat.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 'famat/DESCRIPTION' ... OK
* this is package 'famat' version '1.7.0'
* 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 'famat' 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 ... 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 R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
compl_data   84.02   4.14   88.98
interactions  5.07   0.39   11.42
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  length(hierapath) not equal to 3.
  1/1 mismatches
  [1] 2 - 3 == -1
  ── Failure (test-compl_data.R:23:3): informations are good ─────────────────────
  nrow(inter_values) not equal to 16.
  1/1 mismatches
  [1] 13 - 16 == -3
  ── Failure (test-compl_data.R:25:3): informations are good ─────────────────────
  nrow(sub) not equal to 16.
  1/1 mismatches
  [1] 13 - 16 == -3
  
  [ FAIL 6 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
* 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 ERROR
See
  'F:/biocbuild/bbs-3.16-bioc/meat/famat.Rcheck/00check.log'
for details.


Installation output

famat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/famat_1.7.0.tar.gz && rm -rf famat.buildbin-libdir && mkdir famat.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=famat.buildbin-libdir famat_1.7.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL famat_1.7.0.zip && rm famat_1.7.0.tar.gz famat_1.7.0.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
100 3628k  100 3628k    0     0  12.1M      0 --:--:-- --:--:-- --:--:-- 12.1M
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'famat' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 'famat' as famat_1.7.0.zip
* DONE (famat)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'famat' successfully unpacked and MD5 sums checked

Tests output

famat.Rcheck/tests/testthat.Rout.fail


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(testthat)
> library(famat)

> 
> test_check("famat")
[ FAIL 6 | WARN 0 | SKIP 0 | PASS 6 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-compl_data.R:15:3): informations are good ─────────────────────
nrow(heatmap) not equal to 16.
1/1 mismatches
[1] 13 - 16 == -3
── Failure (test-compl_data.R:17:3): informations are good ─────────────────────
nrow(types) not equal to 12.
1/1 mismatches
[1] 11 - 12 == -1
── Failure (test-compl_data.R:21:3): informations are good ─────────────────────
length(hierabrite) not equal to 3.
1/1 mismatches
[1] 2 - 3 == -1
── Failure (test-compl_data.R:22:3): informations are good ─────────────────────
length(hierapath) not equal to 3.
1/1 mismatches
[1] 2 - 3 == -1
── Failure (test-compl_data.R:23:3): informations are good ─────────────────────
nrow(inter_values) not equal to 16.
1/1 mismatches
[1] 13 - 16 == -3
── Failure (test-compl_data.R:25:3): informations are good ─────────────────────
nrow(sub) not equal to 16.
1/1 mismatches
[1] 13 - 16 == -3

[ FAIL 6 | WARN 0 | SKIP 0 | PASS 6 ]
Error: Test failures
Execution halted

Example timings

famat.Rcheck/famat-Ex.timings

nameusersystemelapsed
compl_data84.02 4.1488.98
interactions 5.07 0.3911.42
path_enrich1.250.081.73
rshiny0.000.010.02