Back to Multiple platform build/check report for BioC 3.18:   simplified   long
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-03-29 11:36:45 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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

Package 684/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
extraChIPs 1.6.1  (landing page)
Stephen Pederson
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/extraChIPs
git_branch: RELEASE_3_18
git_last_commit: fb27d0b
git_last_commit_date: 2024-02-27 06:23:59 -0400 (Tue, 27 Feb 2024)
nebbiolo2Linux (Ubuntu 22.04.3 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
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for extraChIPs on palomino4


To the developers/maintainers of the extraChIPs package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/extraChIPs.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: extraChIPs
Version: 1.6.1
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:extraChIPs.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings extraChIPs_1.6.1.tar.gz
StartedAt: 2024-03-28 00:46:57 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 00:56:02 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 545.5 seconds
RetCode: 0
Status:   OK  
CheckDir: extraChIPs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:extraChIPs.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings extraChIPs_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/extraChIPs.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'extraChIPs/DESCRIPTION' ... OK
* this is package 'extraChIPs' version '1.6.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocParallel', 'GenomicRanges', 'ggplot2', 'ggside',
  'SummarizedExperiment', 'tibble'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'extraChIPs' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.18-bioc/R/library/extraChIPs/libs/x64/extraChIPs.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/extraChIPs.Rcheck/00check.log'
for details.



Installation output

extraChIPs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL extraChIPs
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'extraChIPs' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FMStable.c -o FMStable.o
FMStable.c: In function 'setalpha':
FMStable.c:4835:22: warning: unused variable 'sinhalfangle' [-Wunused-variable]
 4835 |     double sinangle, sinhalfangle;
      |                      ^~~~~~~~~~~~
FMStable.c: In function 'tailsMSS':
FMStable.c:4924:21: warning: unused variable 'temp' [-Wunused-variable]
 4924 |     double z,y,dy,t,temp,scale;
      |                     ^~~~
FMStable.c: At top level:
FMStable.c:231:35: warning: 'alphalarge' defined but not used [-Wunused-variable]
  231 | static int distributiontabulated, alphalarge;
      |                                   ^~~~~~~~~~
FMStable.c:227:52: warning: 'C4' defined but not used [-Wunused-variable]
  227 | static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
      |                                                    ^~
FMStable.c:227:49: warning: 'C3' defined but not used [-Wunused-variable]
  227 | static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
      |                                                 ^~
FMStable.c:227:46: warning: 'C2' defined but not used [-Wunused-variable]
  227 | static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
      |                                              ^~
FMStable.c:227:43: warning: 'C1' defined but not used [-Wunused-variable]
  227 | static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
      |                                           ^~
FMStable.c:227:37: warning: 'angle' defined but not used [-Wunused-variable]
  227 | static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
      |                                     ^~~~~
FMStable.c:227:31: warning: 'ratio' defined but not used [-Wunused-variable]
  227 | static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
      |                               ^~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
gcc -shared -s -static-libgcc -o extraChIPs.dll tmp.def FMStable.o init.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-extraChIPs/00new/extraChIPs/libs/x64
** 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
* DONE (extraChIPs)

Tests output

extraChIPs.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 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(extraChIPs)
Loading required package: BiocParallel
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: ggside
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: tibble
> 
> test_check("extraChIPs")
Creating DGE list...
Calculating experiment-wide normalisation factors...
Estimating dispersions...
Running glmQLFit...
Creating DGE list...
Calculating experiment-wide normalisation factors...
Estimating dispersions...
Running glmQLFit...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 575 ]
> 
> proc.time()
   user  system elapsed 
  77.40    3.10   82.73 

Example timings

extraChIPs.Rcheck/extraChIPs-Ex.timings

nameusersystemelapsed
addDiffStatus-methods1.380.001.38
as_tibble0.560.020.57
bestOverlap-methods1.160.091.25
chopMC0.170.000.17
colToRanges-methods0.210.000.21
collapseGenes000
cytobands0.030.030.06
defineRegions3.640.053.69
defineSeqinfo0.010.030.04
distinctMC0.380.020.39
dualFilter000
ex_datasets0.000.010.01
fitAssayDiff-methods0.280.000.28
fixed_width_datasets0.030.020.06
getProfileData-methods1.640.001.69
grlToSE-methods0.470.020.48
importPeaks0.20.00.2
makeConsensus1.250.011.27
mapByFeature0.770.000.76
mapGrlCols2.090.022.11
mergeByCol-methods0.310.010.33
mergeByHMP-methods0.410.000.40
mergeBySig-methods0.650.000.68
partitionRanges-methods1.540.001.53
plotAssayDensities-methods1.390.021.40
plotAssayHeatmap-methods0.390.000.39
plotAssayPCA-methods0.900.050.96
plotAssayRle-methods0.890.010.90
plotGrlCol1.360.051.41
plotHFGC000
plotOverlaps-methods2.610.022.63
plotPairwise3.300.013.31
plotPie-methods1.620.051.67
plotProfileHeatmap-methods000
plotSplitDonut-methods1.350.031.39
propOverlap-methods0.250.000.25
reduceMC0.230.010.25
setoptsMC-methods0.830.000.83
stitchRanges0.280.000.30
voomWeightsFromCPM0.240.000.71