| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:20 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| 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 684/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| extraChIPs 1.6.1 (landing page) Stephen Pederson
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: extraChIPs |
| Version: 1.6.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:extraChIPs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings extraChIPs_1.6.1.tar.gz |
| StartedAt: 2024-03-03 20:33:14 -0500 (Sun, 03 Mar 2024) |
| EndedAt: 2024-03-03 20:43:12 -0500 (Sun, 03 Mar 2024) |
| EllapsedTime: 597.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: extraChIPs.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:extraChIPs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings extraChIPs_1.6.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/extraChIPs.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘extraChIPs’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 is not available
* 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
‘/Users/biocbuild/bbs-3.18-bioc/meat/extraChIPs.Rcheck/00check.log’
for details.
extraChIPs.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL extraChIPs
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘extraChIPs’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FMStable.c -o FMStable.o
FMStable.c:4835:22: warning: unused variable 'sinhalfangle' [-Wunused-variable]
double sinangle, sinhalfangle;
^
FMStable.c:4924:21: warning: unused variable 'temp' [-Wunused-variable]
double z,y,dy,t,temp,scale;
^
FMStable.c:227:31: warning: unused variable 'ratio' [-Wunused-variable]
static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
^
FMStable.c:227:37: warning: unused variable 'angle' [-Wunused-variable]
static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
^
FMStable.c:227:43: warning: unused variable 'C1' [-Wunused-variable]
static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
^
FMStable.c:227:46: warning: unused variable 'C2' [-Wunused-variable]
static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
^
FMStable.c:227:49: warning: unused variable 'C3' [-Wunused-variable]
static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
^
FMStable.c:227:52: warning: unused variable 'C4' [-Wunused-variable]
static double Clogd,alphastar,ratio,angle,C1,C2,C3,C4,eta;
^
FMStable.c:231:35: warning: unused variable 'alphalarge' [-Wunused-variable]
static int distributiontabulated, alphalarge;
^
9 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o extraChIPs.so FMStable.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-extraChIPs/00new/extraChIPs/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (extraChIPs)
extraChIPs.Rcheck/tests/testthat.Rout
R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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
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
81.053 2.943 84.935
extraChIPs.Rcheck/extraChIPs-Ex.timings
| name | user | system | elapsed | |
| addDiffStatus-methods | 1.453 | 0.034 | 1.499 | |
| as_tibble | 0.540 | 0.012 | 0.557 | |
| bestOverlap-methods | 1.223 | 0.085 | 1.318 | |
| chopMC | 0.170 | 0.002 | 0.173 | |
| colToRanges-methods | 0.229 | 0.002 | 0.231 | |
| collapseGenes | 0.003 | 0.001 | 0.004 | |
| cytobands | 0.015 | 0.006 | 0.021 | |
| defineRegions | 4.501 | 0.041 | 4.572 | |
| defineSeqinfo | 0.009 | 0.002 | 0.011 | |
| distinctMC | 0.299 | 0.002 | 0.300 | |
| dualFilter | 0 | 0 | 0 | |
| ex_datasets | 0.013 | 0.002 | 0.015 | |
| fitAssayDiff-methods | 0.225 | 0.012 | 0.239 | |
| fixed_width_datasets | 0.065 | 0.006 | 0.072 | |
| getProfileData-methods | 1.785 | 0.018 | 1.828 | |
| grlToSE-methods | 0.570 | 0.008 | 0.582 | |
| importPeaks | 0.168 | 0.005 | 0.173 | |
| makeConsensus | 1.115 | 0.016 | 1.139 | |
| mapByFeature | 0.836 | 0.012 | 0.856 | |
| mapGrlCols | 1.835 | 0.017 | 1.865 | |
| mergeByCol-methods | 0.403 | 0.005 | 0.410 | |
| mergeByHMP-methods | 0.555 | 0.006 | 0.568 | |
| mergeBySig-methods | 0.564 | 0.011 | 0.579 | |
| partitionRanges-methods | 1.251 | 0.011 | 1.268 | |
| plotAssayDensities-methods | 1.261 | 0.046 | 1.318 | |
| plotAssayHeatmap-methods | 0.518 | 0.008 | 0.531 | |
| plotAssayPCA-methods | 0.905 | 0.016 | 0.929 | |
| plotAssayRle-methods | 1.036 | 0.015 | 1.060 | |
| plotGrlCol | 1.704 | 0.031 | 1.750 | |
| plotHFGC | 0 | 0 | 0 | |
| plotOverlaps-methods | 3.407 | 0.056 | 3.495 | |
| plotPairwise | 3.625 | 0.043 | 3.692 | |
| plotPie-methods | 1.812 | 0.032 | 1.860 | |
| plotProfileHeatmap-methods | 0.000 | 0.000 | 0.001 | |
| plotSplitDonut-methods | 1.724 | 0.026 | 1.765 | |
| propOverlap-methods | 0.385 | 0.002 | 0.388 | |
| reduceMC | 0.311 | 0.004 | 0.318 | |
| setoptsMC-methods | 1.167 | 0.015 | 1.195 | |
| stitchRanges | 0.323 | 0.003 | 0.328 | |
| voomWeightsFromCPM | 0.267 | 0.012 | 0.285 | |