Back to Long Tests report for BioC 3.14

This page was generated on 2022-04-09 21:00:03 -0400 (Sat, 09 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4322
riesling1Windows Server 2019 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4108
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4135
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

CHECK results for ChromSCape on riesling1


To the developers/maintainers of the ChromSCape package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 11/19HostnameOS / ArchCHECK
ChromSCape 1.4.0  (landing page)
Pacome Prompsy
Snapshot Date: 2022-04-09 06:55:01 -0400 (Sat, 09 Apr 2022)
git_url: https://git.bioconductor.org/packages/ChromSCape
git_branch: RELEASE_3_14
git_last_commit: df9f2c5
git_last_commit_date: 2021-10-26 13:03:23 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  ERROR  
riesling1Windows Server 2019 Standard / x64  ERROR  
machv2macOS 10.14.6 Mojave / x86_64  ERROR  

Summary

Package: ChromSCape
Version: 1.4.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no ChromSCape_1.4.0.tar.gz
StartedAt: 2022-04-09 08:06:33 -0400 (Sat, 09 Apr 2022)
EndedAt: 2022-04-09 08:18:26 -0400 (Sat, 09 Apr 2022)
EllapsedTime: 713.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: ChromSCape.Rcheck
Warnings: NA

Tests output

ChromSCape.Rcheck/tests_i386/testthat.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(ChromSCape)
> 
> test_check("ChromSCape")
[1] "Running Batch Correction ..."
== Failed tests ================================================================
-- Failure (test_correlation_clustering.R:99:3): Choosing clusters - Wrong inputs. --
`choose_cluster_scExp(scExp_cf.)` did not throw an error.
-- Error (test_diff_analysis_gene_set_enrichment.R:44:1): (code run outside of `test_that()`) --
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'normcounts': invalid or not-yet-implemented 'Matrix' subsetting
Backtrace:
     x
  1. +-ChromSCape::differential_analysis_scExp(...) test_diff_analysis_gene_set_enrichment.R:44:0
  2. | +-SingleCellExperiment::normcounts(...)
  3. | +-scExp[SingleCellExperiment::rowData(scExp)$top_feature, ]
  4. | \-scExp[SingleCellExperiment::rowData(scExp)$top_feature, ]
  5. |   +-methods::callNextMethod()
  6. |   \-SummarizedExperiment:::.nextMethod(x = x, i = i, j = )
  7. |     +-x@assays[ii, ]
  8. |     \-x@assays[ii, ]
  9. |       \-SummarizedExperiment:::.extract_Assays_subset(x, i, j)
 10. |         +-methods::as(endoapply(assays, extract_assay_subset), class(x))
 11. |         | \-methods:::.class1(object)
 12. |         \-S4Vectors::endoapply(assays, extract_assay_subset)
 13. |           +-BiocGenerics::lapply(X, FUN, ...)
 14. |           \-S4Vectors::lapply(X, FUN, ...)
 15. |             +-BiocGenerics::lapply(as.list(X), match.fun(FUN), ...)
 16. |             \-base::lapply(as.list(X), match.fun(FUN), ...)
 17. |               \-SummarizedExperiment:::FUN(X[[i]], ...)
 18. |                 +-BiocGenerics::do.call(`[`, args)
 19. |                 +-base::do.call(`[`, args)
 20. |                 +-.Primitive("[")(...)
 21. |                 \-.Primitive("[")(...)
 22. |                   \-base::stop("invalid or not-yet-implemented 'Matrix' subsetting")
 23. \-base::.handleSimpleError(...)
 24.   \-base:::h(simpleError(msg, call))

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 82 ]
Error: Test failures
Execution halted

ChromSCape.Rcheck/tests_x64/testthat.Rout.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(ChromSCape)
> 
> test_check("ChromSCape")
[1] "Running Batch Correction ..."
== Failed tests ================================================================
-- Failure (test_correlation_clustering.R:99:3): Choosing clusters - Wrong inputs. --
`choose_cluster_scExp(scExp_cf.)` did not throw an error.
-- Error (test_diff_analysis_gene_set_enrichment.R:44:1): (code run outside of `test_that()`) --
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'normcounts': invalid or not-yet-implemented 'Matrix' subsetting
Backtrace:
     x
  1. +-ChromSCape::differential_analysis_scExp(...) test_diff_analysis_gene_set_enrichment.R:44:0
  2. | +-SingleCellExperiment::normcounts(...)
  3. | +-scExp[SingleCellExperiment::rowData(scExp)$top_feature, ]
  4. | \-scExp[SingleCellExperiment::rowData(scExp)$top_feature, ]
  5. |   +-methods::callNextMethod()
  6. |   \-SummarizedExperiment:::.nextMethod(x = x, i = i, j = )
  7. |     +-x@assays[ii, ]
  8. |     \-x@assays[ii, ]
  9. |       \-SummarizedExperiment:::.extract_Assays_subset(x, i, j)
 10. |         +-methods::as(endoapply(assays, extract_assay_subset), class(x))
 11. |         | \-methods:::.class1(object)
 12. |         \-S4Vectors::endoapply(assays, extract_assay_subset)
 13. |           +-BiocGenerics::lapply(X, FUN, ...)
 14. |           \-S4Vectors::lapply(X, FUN, ...)
 15. |             +-BiocGenerics::lapply(as.list(X), match.fun(FUN), ...)
 16. |             \-base::lapply(as.list(X), match.fun(FUN), ...)
 17. |               \-SummarizedExperiment:::FUN(X[[i]], ...)
 18. |                 +-BiocGenerics::do.call(`[`, args)
 19. |                 +-base::do.call(`[`, args)
 20. |                 +-.Primitive("[")(...)
 21. |                 \-.Primitive("[")(...)
 22. |                   \-base::stop("invalid or not-yet-implemented 'Matrix' subsetting")
 23. \-base::.handleSimpleError(...)
 24.   \-base:::h(simpleError(msg, call))

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 82 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no ChromSCape_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc-longtests/meat/ChromSCape.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'ChromSCape/DESCRIPTION' ... OK
* this is package 'ChromSCape' version '1.4.0'
* 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 ... 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 'ChromSCape' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.0Mb
    www    2.1Mb
* checking package 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
CompareWilcox: no visible binding for global variable 'annot.'
bams_to_matrix_indexes: no visible binding for global variable
  'files_dir_list'
filter_correlated_cell_scExp: no visible binding for global variable
  'run_tsne'
generate_analysis: no visible binding for global variable 'k'
generate_analysis: no visible binding for global variable
  'clusterConsensus'
get_most_variable_cyto: no visible binding for global variable
  'cytoBand'
get_most_variable_cyto: no visible binding for global variable
  'Fri_cyto'
num_cell_after_QC_filt_scExp: no visible binding for global variable
  'sample_id'
num_cell_after_QC_filt_scExp: no visible binding for global variable
  'total_counts'
num_cell_scExp: no visible binding for global variable 'sample_id'
num_cell_scExp: no visible binding for global variable 'total_counts'
plot_gain_or_loss_barplots: no visible binding for global variable
  'Gain_or_Loss'
plot_gain_or_loss_barplots: no visible binding for global variable
  'ncells'
plot_gain_or_loss_barplots: no visible binding for global variable
  'cytoBand'
plot_most_contributing_features: no visible binding for global variable
  'genes'
plot_pie_most_contributing_chr: no visible binding for global variable
  'absolute_value'
plot_reduced_dim_scExp: no visible binding for global variable 'V1'
plot_reduced_dim_scExp: no visible binding for global variable 'V2'
plot_reduced_dim_scExp: no visible binding for global variable
  'cluster'
subset_bam_call_peaks: no visible binding for global variable
  'merged_bam'
Undefined global functions or variables:
  Fri_cyto Gain_or_Loss V1 V2 absolute_value annot. cluster
  clusterConsensus cytoBand files_dir_list genes k merged_bam ncells
  run_tsne sample_id total_counts
* checking Rd files ... NOTE
prepare_Rd: raw_counts_to_sparse_matrix.Rd:6-8: Dropping empty section \source
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* 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 ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
   14. |           \-S4Vectors::lapply(X, FUN, ...)
   15. |             +-BiocGenerics::lapply(as.list(X), match.fun(FUN), ...)
   16. |             \-base::lapply(as.list(X), match.fun(FUN), ...)
   17. |               \-SummarizedExperiment:::FUN(X[[i]], ...)
   18. |                 +-BiocGenerics::do.call(`[`, args)
   19. |                 +-base::do.call(`[`, args)
   20. |                 +-.Primitive("[")(...)
   21. |                 \-.Primitive("[")(...)
   22. |                   \-base::stop("invalid or not-yet-implemented 'Matrix' subsetting")
   23. \-base::.handleSimpleError(...)
   24.   \-base:::h(simpleError(msg, call))
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 82 ]
  Error: Test failures
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
   14. |           \-S4Vectors::lapply(X, FUN, ...)
   15. |             +-BiocGenerics::lapply(as.list(X), match.fun(FUN), ...)
   16. |             \-base::lapply(as.list(X), match.fun(FUN), ...)
   17. |               \-SummarizedExperiment:::FUN(X[[i]], ...)
   18. |                 +-BiocGenerics::do.call(`[`, args)
   19. |                 +-base::do.call(`[`, args)
   20. |                 +-.Primitive("[")(...)
   21. |                 \-.Primitive("[")(...)
   22. |                   \-base::stop("invalid or not-yet-implemented 'Matrix' subsetting")
   23. \-base::.handleSimpleError(...)
   24.   \-base:::h(simpleError(msg, call))
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 82 ]
  Error: Test failures
  Execution halted
* DONE

Status: 2 ERRORs, 4 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc-longtests/meat/ChromSCape.Rcheck/00check.log'
for details.


Installation output

ChromSCape.Rcheck/00install.out

* installing *source* package 'ChromSCape' ...
** using staged installation
** libs

*** arch - i386
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c as_dist.cpp -o as_dist.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ChromSCape.dll tmp.def RcppExports.o as_dist.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc-longtests/meat/ChromSCape.Rcheck/00LOCK-ChromSCape/00new/ChromSCape/libs/i386

*** arch - x64
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c as_dist.cpp -o as_dist.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ChromSCape.dll tmp.def RcppExports.o as_dist.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/ChromSCape.Rcheck/00_pkg_src/ChromSCape/src-x64/RcppExports.o: file format not recognized
C:\rtools40\mingw32\bin\nm.exe: D:/biocbuild/bbs-3.14-bioc-longtests/meat/ChromSCape.Rcheck/00_pkg_src/ChromSCape/src-x64/as_dist.o: file format not recognized
Warning messages:
1: In system(sprintf("%s -Pg %s", nm, shQuote(f)), intern = TRUE) :
  running command 'C:\rtools40\mingw32\bin\nm.exe -Pg "D:/biocbuild/bbs-3.14-bioc-longtests/meat/ChromSCape.Rcheck/00_pkg_src/ChromSCape/src-x64/RcppExports.o"' had status 1
2: In system(sprintf("%s -Pg %s", nm, shQuote(f)), intern = TRUE) :
  running command 'C:\rtools40\mingw32\bin\nm.exe -Pg "D:/biocbuild/bbs-3.14-bioc-longtests/meat/ChromSCape.Rcheck/00_pkg_src/ChromSCape/src-x64/as_dist.o"' had status 1
installing to D:/biocbuild/bbs-3.14-bioc-longtests/meat/ChromSCape.Rcheck/00LOCK-ChromSCape/00new/ChromSCape/libs/x64
** 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
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (ChromSCape)