Altuna Akalin
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/genomation |
| git_branch: RELEASE_3_17 |
| git_last_commit: f8dc939 |
| git_last_commit_date: 2023-04-25 10:36:42 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:23 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 798/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| genomation 1.32.0 (landing page) Altuna Akalin
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the genomation package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genomation.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: genomation |
| Version: 1.32.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:genomation.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings genomation_1.32.0.tar.gz |
| StartedAt: 2023-10-15 21:34:11 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 21:39:32 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 321.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genomation.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:genomation.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings genomation_1.32.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/genomation.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘genomation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomation’ version ‘1.32.0’
* package encoding: latin1
* 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 ‘genomation’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
See ‘/home/biocbuild/bbs-3.17-bioc/meat/genomation.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
in ScoreMatrixBin() function.
Cannot process chunk/lines:
NEW FUNCTIONS AND FEATURES
Cannot process chunk/lines:
The character vectors will label the x-axis of heatmaps. Examples: xcoords=c("-2kb","0","2kb")
Cannot process chunk/lines:
Implemented by Bozena Mika-Gospodorz.
Cannot process chunk/lines:
Implemented by Bozena Mika-Gospodorz.
Cannot process chunk/lines:
Implemented by Bozena Mika-Gospodorz.
Cannot process chunk/lines:
Implemented by Bozena Mika-Gospodorz.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ScoreMatrixBin,RleList-GRangesList: no visible binding for global
variable ‘id’
ScoreMatrixBin,RleList-GRangesList: no visible global function
definition for ‘:=’
Undefined global functions or variables:
:= id
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
enrichmentMatrix-ScoreMatrixList-method 6.776 3.018 6.163
enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method 4.441 0.649 6.666
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘genomation_unit_tests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘GenomationManual.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/genomation.Rcheck/00check.log’
for details.
genomation.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL genomation ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘genomation’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c binSum.cpp -o binSum.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o genomation.so RcppExports.o binSum.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-genomation/00new/genomation/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’ ** testing if installed package keeps a record of temporary installation path * DONE (genomation)
genomation.Rcheck/tests/genomation_unit_tests.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.
> (require("genomation") & require("GenomicRanges") & require("GenomicAlignments") & require("rtracklayer") & require("readr") & require("Biostrings")) || stop("unable to load genomation package")
Loading required package: genomation
Loading required package: grid
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: GenomicAlignments
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: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:grid':
pattern
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
Loading required package: rtracklayer
Loading required package: readr
[1] TRUE
Warning message:
replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation'
> genomation:::.test()
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
testing:min
testing:max
testing:median
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Normalizing to rpm ...
Rows: 2 Columns: 9
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (3): X1, X4, X6
dbl (5): X2, X3, X5, X7, X8
num (1): X9
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2 Columns: 9
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (3): X1, X4, X6
dbl (5): X2, X3, X5, X7, X8
num (1): X9
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
RUNIT TEST PROTOCOL -- Sun Oct 15 21:39:03 2023
***********************************************
Number of test functions: 24
Number of errors: 0
Number of failures: 0
1 Test Suite :
genomation RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24
Number of errors: 0
Number of failures: 0
Warning messages:
1: In .local(target, windows, strand.aware) :
1 windows fall off the target
2: In .local(target, windows, strand.aware) :
2 windows fall off the target
3: In .local(target, windows, strand.aware) :
2 windows fall off the target
4: In .local(target, windows, strand.aware) :
2 windows fall off the target
5: In .local(target, windows, strand.aware) :
2 windows fall off the target
6: In .local(target, windows, strand.aware) :
2 windows fall off the target
7: In .local(target, windows, bin.num, bin.op, strand.aware) :
2 windows fall off the target
8: In .local(target, windows, bin.num, bin.op, strand.aware) :
2 windows fall off the target
>
> proc.time()
user system elapsed
26.390 1.917 27.964
genomation.Rcheck/genomation-Ex.timings
| name | user | system | elapsed | |
| AnnotationByGeneParts-methods | 1.531 | 0.012 | 1.553 | |
| ScoreMatrix-methods | 1.373 | 0.104 | 1.478 | |
| ScoreMatrixBin-methods | 1.669 | 0.067 | 1.722 | |
| ScoreMatrixList-methods | 0.442 | 0.011 | 0.453 | |
| annotateWithFeature-methods | 0.034 | 0.003 | 0.038 | |
| annotateWithFeatureFlank-methods | 0.286 | 0.001 | 0.286 | |
| annotateWithFeatures-methods | 0.567 | 0.016 | 0.543 | |
| annotateWithGeneParts-methods | 0.396 | 0.016 | 0.424 | |
| binMatrix-methods | 0.157 | 0.004 | 0.162 | |
| convertBed2Exons-methods | 0.048 | 0.000 | 0.048 | |
| convertBed2Introns-methods | 0.045 | 0.000 | 0.045 | |
| enrichmentMatrix-ScoreMatrix-method | 3.101 | 0.076 | 3.249 | |
| enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method | 4.441 | 0.649 | 6.666 | |
| enrichmentMatrix-ScoreMatrixList-method | 6.776 | 3.018 | 6.163 | |
| findFeatureComb-methods | 1.232 | 1.077 | 0.376 | |
| getFeatsWithTargetsStats-methods | 0.348 | 0.037 | 0.376 | |
| getFlanks-methods | 0.165 | 0.018 | 0.183 | |
| getRandomEnrichment-methods | 0.005 | 0.000 | 0.004 | |
| getTargetAnnotationStats-methods | 0.334 | 0.057 | 0.382 | |
| gffToGRanges | 0.114 | 0.011 | 0.126 | |
| heatMatrix | 0.213 | 0.083 | 0.298 | |
| heatMeta | 0.342 | 0.025 | 0.366 | |
| heatTargetAnnotation-methods | 0.593 | 0.055 | 0.610 | |
| intersectScoreMatrixList-methods | 0.240 | 0.008 | 0.248 | |
| multiHeatMatrix | 0.319 | 0.052 | 0.371 | |
| orderBy-methods | 0.421 | 0.016 | 0.437 | |
| patternMatrix-methods | 0.124 | 0.000 | 0.124 | |
| plotMeta | 0.322 | 0.004 | 0.326 | |
| plotTargetAnnotation-methods | 0.307 | 0.032 | 0.332 | |
| readBed | 0.124 | 0.051 | 0.160 | |
| readBroadPeak | 0.033 | 0.016 | 0.043 | |
| readFeatureFlank-methods | 0.168 | 0.024 | 0.190 | |
| readGeneric | 0.035 | 0.024 | 0.050 | |
| readNarrowPeak | 0.036 | 0.019 | 0.049 | |
| readTranscriptFeatures-methods | 0.185 | 0.024 | 0.201 | |
| scaleScoreMatrix-methods | 0.171 | 0.004 | 0.175 | |
| scaleScoreMatrixList | 0.489 | 0.040 | 0.530 | |