| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:16 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 1562/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| plotgardener 1.8.3 (landing page) Nicole Kramer
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | WARNINGS | OK |  | |||||||
|
To the developers/maintainers of the plotgardener package: - 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: plotgardener |
| Version: 1.8.3 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:plotgardener.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings plotgardener_1.8.3.tar.gz |
| StartedAt: 2024-04-17 23:12:31 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 23:19:41 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 429.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: plotgardener.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:plotgardener.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings plotgardener_1.8.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/plotgardener.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plotgardener/DESCRIPTION’ ... OK
* this is package ‘plotgardener’ version ‘1.8.3’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘plotgardener’ can be installed ... WARNING
Found the following significant warnings:
checkRow.cpp:19:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
checkRow.cpp:20:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
checkRow.cpp:22:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
checkRow.cpp:21:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
checkRow.cpp:20:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/plotgardener.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘GenomeInfoDb’ ‘GenomicRanges’
A package should be listed in only one of these fields.
* 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 startup messages can be suppressed ... 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
pgParams: no visible binding for global variable ‘width’
pgParams: no visible binding for global variable ‘strand’
Undefined global functions or variables:
strand width
* 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 R/sysdata.rda ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotRaster 12.686 0.606 13.351
plotIdeogram 6.590 0.439 8.977
plotGenes 5.107 0.171 5.299
* 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 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/plotgardener.Rcheck/00check.log’
for details.
plotgardener.Rcheck/00install.out
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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL plotgardener
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘plotgardener’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c checkRow.cpp -o checkRow.o
checkRow.cpp:19:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if (((v[rowCol] == j) &
~^~~~~~~~~~~~~~~~~~
&&
checkRow.cpp:19:12: note: cast one or both operands to int to silence this warning
checkRow.cpp:20:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
(((start >= v[0]) & (start <= v[1])) |
~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
checkRow.cpp:20:12: note: cast one or both operands to int to silence this warning
checkRow.cpp:22:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
((start <= v[0]) & (stop >= v[1]))))){
~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
checkRow.cpp:22:12: note: cast one or both operands to int to silence this warning
checkRow.cpp:20:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
(((start >= v[0]) & (start <= v[1])) |
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
checkRow.cpp:20:12: note: cast one or both operands to int to silence this warning
checkRow.cpp:21:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
((stop >= v[0]) & (stop <= v[1])) |
~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
checkRow.cpp:21:12: note: cast one or both operands to int to silence this warning
checkRow.cpp:20:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
(((start >= v[0]) & (start <= v[1])) |
~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
checkRow.cpp:20:13: note: cast one or both operands to int to silence this warning
6 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rebinBigwig.cpp -o rebinBigwig.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o plotgardener.so RcppExports.o checkRow.o rebinBigwig.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-plotgardener/00new/plotgardener/libs
** R
** 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 (plotgardener)
plotgardener.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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(plotgardener)
Attaching package: 'plotgardener'
The following object is masked from 'package:base':
c
>
> test_check("plotgardener")
Loading required package: GenomicFeatures
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
Loading required package: stats4
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: GenomicRanges
Loading required package: AnnotationDbi
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")'.
Using poppler version 23.04.0
Loading required package: BiocFileCache
Loading required package: dbplyr
Attaching package: 'AnnotationHub'
The following object is masked from 'package:Biobase':
cache
pairs[pairs1]
arches[arches1]
ranges[ranges1]
transcripts[transcripts1]
start, endLoading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
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
The following object is masked from 'package:Biobase':
rowMedians
Read in hic file with KR normalization at 1e+05 BP resolution.
signal[signal1_h]
signal[signal1_h]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 118 ]
>
> proc.time()
user system elapsed
54.468 2.655 58.833
plotgardener.Rcheck/plotgardener-Ex.timings
| name | user | system | elapsed | |
| annoDomains | 1.938 | 0.058 | 2.012 | |
| annoGenomeLabel | 3.361 | 0.180 | 3.574 | |
| annoHeatmapLegend | 1.717 | 0.036 | 1.754 | |
| annoHighlight | 0.934 | 0.047 | 0.983 | |
| annoPixels | 1.024 | 0.064 | 1.094 | |
| annoSegments | 2.462 | 0.072 | 2.538 | |
| annoText | 1.318 | 0.044 | 1.407 | |
| annoXaxis | 1.527 | 0.056 | 1.604 | |
| annoYaxis | 0.679 | 0.051 | 0.739 | |
| annoZoomLines | 3.222 | 0.120 | 3.387 | |
| assembly | 0.000 | 0.001 | 0.000 | |
| c | 0.000 | 0.000 | 0.001 | |
| calcSignalRange | 0.470 | 0.022 | 0.495 | |
| colorby | 0.970 | 0.010 | 0.983 | |
| defaultPackages | 0.011 | 0.000 | 0.011 | |
| genomes | 0.000 | 0.000 | 0.001 | |
| mapColors | 0.076 | 0.004 | 0.080 | |
| pageCreate | 0.042 | 0.002 | 0.044 | |
| pageGuideHide | 0.034 | 0.002 | 0.036 | |
| pageGuideHorizontal | 0.031 | 0.001 | 0.033 | |
| pageGuideShow | 0.936 | 0.069 | 1.021 | |
| pageGuideVertical | 0.133 | 0.004 | 0.136 | |
| pageLayoutCol | 0.001 | 0.001 | 0.002 | |
| pageLayoutRow | 0.000 | 0.000 | 0.001 | |
| pagePlotPlace | 0.702 | 0.050 | 0.769 | |
| pagePlotRemove | 0.570 | 0.030 | 0.603 | |
| pgParams | 2.097 | 0.123 | 2.232 | |
| plotCircle | 0.030 | 0.002 | 0.032 | |
| plotGG | 0.256 | 0.009 | 0.267 | |
| plotGenes | 5.107 | 0.171 | 5.299 | |
| plotGenomeLabel | 1.917 | 0.079 | 2.039 | |
| plotHicRectangle | 0.486 | 0.030 | 0.524 | |
| plotHicSquare | 0.758 | 0.046 | 0.809 | |
| plotHicTriangle | 1.398 | 0.067 | 1.468 | |
| plotIdeogram | 6.590 | 0.439 | 8.977 | |
| plotLegend | 0.359 | 0.016 | 0.389 | |
| plotManhattan | 2.436 | 0.092 | 2.556 | |
| plotMultiSignal | 2.305 | 0.077 | 2.404 | |
| plotPairs | 0.141 | 0.008 | 0.150 | |
| plotPairsArches | 0.127 | 0.007 | 0.135 | |
| plotPolygon | 0.053 | 0.002 | 0.056 | |
| plotRanges | 0.194 | 0.010 | 0.205 | |
| plotRaster | 12.686 | 0.606 | 13.351 | |
| plotRect | 0.878 | 0.042 | 0.920 | |
| plotSegments | 0.065 | 0.003 | 0.069 | |
| plotSignal | 0.930 | 0.049 | 0.981 | |
| plotText | 0.061 | 0.003 | 0.065 | |
| plotTranscripts | 0.953 | 0.034 | 0.989 | |
| readBigwig | 0.297 | 0.007 | 0.304 | |
| readHic | 0.009 | 0.002 | 0.012 | |