| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-27 05:50:29 -0000 (Mon, 27 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6083 |
| 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 | ||||
|
To the developers/maintainers of the BASiCS package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BASiCS.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. |
| Package 129/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BASiCS 2.11.9 (landing page) Catalina Vallejos
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: BASiCS |
| Version: 2.11.9 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BASiCS_2.11.9.tar.gz |
| StartedAt: 2023-03-24 21:16:10 -0000 (Fri, 24 Mar 2023) |
| EndedAt: 2023-03-24 21:24:15 -0000 (Fri, 24 Mar 2023) |
| EllapsedTime: 484.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: BASiCS.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BASiCS_2.11.9.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BASiCS.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BASiCS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BASiCS’ version ‘2.11.9’
* 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 ‘BASiCS’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 11.2Mb
sub-directories of 1Mb or more:
data 2.0Mb
libs 8.2Mb
* 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 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 ... 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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
BASiCS_MCMC 9.419 0.832 10.524
BASiCS_TestDE 8.997 0.043 9.044
newBASiCS_Chain 5.395 0.172 5.567
BASiCS_Chain 5.182 0.240 5.424
BASiCS_Chain-methods 3.974 0.811 5.227
BASiCS_DivideAndConquer 3.712 0.074 26.174
* 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:
Offset estimate: 0.6714
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6787
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘BASiCS.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/BASiCS.Rcheck/00check.log’
for details.
BASiCS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BASiCS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘BASiCS’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c BASiCS.cpp -o BASiCS.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -shared -L/usr/local/lib -o BASiCS.so BASiCS.o RcppExports.o -llapack -L/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/lib -lRblas -lgfortran -lm -fopenmp installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-BASiCS/00new/BASiCS/libs ** R ** data ** inst ** 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 ** 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 (BASiCS)
BASiCS.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> library(testthat)
> library(BASiCS)
Loading required package: SingleCellExperiment
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: 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 objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
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
Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
Bioconductor, please visit:
https://github.com/catavallejos/BASiCS/wiki.
>
> test_check("BASiCS")
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio SC vs P&S).
-------------------------------------------------------------
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio Group1 vs Group2).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
For Differential mean task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task.
Probability threshold automatically set equal to 'ProbThresholdD'.
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio Group1 vs Group2).
-------------------------------------------------------------
For Differential mean task:
the posterior probability threshold chosen via EFDR calibration is too low.
Probability threshold automatically set equal to 'ProbThresholdM'.
EFDR calibration failed for Differential dispersion task.
Probability threshold automatically set equal to 'ProbThresholdD'.
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6714
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
-------------------------------------------------------------
Log-fold change thresholds are now set in a log2 scale.
Original BASiCS release used a natural logarithm scale.
-------------------------------------------------------------
Offset estimate: 0.6787
(ratio SC vs P&S).
To visualise its effect, please use 'PlotOffset = TRUE'.
-------------------------------------------------------------
Killed
BASiCS.Rcheck/BASiCS-Ex.timings
| name | user | system | elapsed | |
| BASiCS_Chain-methods | 3.974 | 0.811 | 5.227 | |
| BASiCS_Chain | 5.182 | 0.240 | 5.424 | |
| BASiCS_CorrectOffset | 0.020 | 0.000 | 0.023 | |
| BASiCS_DenoisedCounts | 3.230 | 0.059 | 3.290 | |
| BASiCS_DenoisedRates | 3.109 | 0.072 | 3.181 | |
| BASiCS_DetectVG | 1.013 | 0.028 | 1.045 | |
| BASiCS_DiagHist | 1.415 | 0.016 | 1.455 | |
| BASiCS_DiagPlot | 2.551 | 0.824 | 4.209 | |
| BASiCS_DivideAndConquer | 3.712 | 0.074 | 26.174 | |
| BASiCS_Draw | 0.562 | 0.019 | 0.584 | |
| BASiCS_EffectiveSize | 0.281 | 0.027 | 0.313 | |
| BASiCS_Filter | 0.003 | 0.000 | 0.003 | |
| BASiCS_LoadChain | 2.783 | 0.193 | 3.013 | |
| BASiCS_MCMC | 9.419 | 0.832 | 10.524 | |
| BASiCS_MockSCE | 0.531 | 0.004 | 0.535 | |
| BASiCS_PlotDE | 4.561 | 0.103 | 4.667 | |
| BASiCS_PlotOffset | 1.268 | 0.003 | 1.272 | |
| BASiCS_PlotVG | 0.518 | 0.008 | 0.525 | |
| BASiCS_PriorParam | 0.409 | 0.000 | 0.409 | |
| BASiCS_ShowFit | 0.324 | 0.000 | 0.326 | |
| BASiCS_Sim | 1.175 | 0.000 | 1.176 | |
| BASiCS_Summary-methods | 0.006 | 0.000 | 0.007 | |
| BASiCS_Summary | 2.854 | 0.080 | 2.935 | |
| BASiCS_TestDE | 8.997 | 0.043 | 9.044 | |
| BASiCS_VarThresholdSearchHVG_LVG | 3.047 | 0.044 | 3.092 | |
| BASiCS_VarianceDecomp | 0.299 | 0.007 | 0.306 | |
| Summary-BASiCS_Chain-method | 0.069 | 0.004 | 0.073 | |
| dim-BASiCS_Chain-method | 0.008 | 0.000 | 0.008 | |
| dimnames-BASiCS_Chain-method | 0.006 | 0.002 | 0.008 | |
| displayChainBASiCS-BASiCS_Chain-method | 0.144 | 0.028 | 0.281 | |
| displaySummaryBASiCS-BASiCS_Summary-method | 0.127 | 0.017 | 0.145 | |
| makeExampleBASiCS_Data | 0.428 | 0.004 | 0.432 | |
| newBASiCS_Chain | 5.395 | 0.172 | 5.567 | |
| plot-BASiCS_Chain-method | 0.132 | 0.008 | 0.141 | |
| plot-BASiCS_Summary-method | 0.124 | 0.015 | 0.139 | |
| show-BASiCS_ResultDE-method | 0.119 | 0.019 | 0.139 | |
| show-BASiCS_ResultVG-method | 0.127 | 0.012 | 0.139 | |
| show-BASiCS_ResultsDE-method | 0.135 | 0.004 | 0.138 | |
| subset-BASiCS_Chain-method | 1.213 | 0.012 | 1.225 | |