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HenrikBengtsson / matrixStats

R package: Methods that Apply to Rows and Columns of Matrices (and to Vectors)
https://cran.r-project.org/package=matrixStats
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CRAN check error on R version 4.3.0 beta (2023-04-07 r84200 ucrt) for MS Windows #231

Closed HenrikBengtsson closed 1 year ago

HenrikBengtsson commented 1 year ago

I doubt the below CRAN check error that just popped up is a problem with matrixStats. I suspect (=hope) it's an issue with the R 4.3.0 beta version. I'm just logging it here for the record.

From https://www.r-project.org/nosvn/R.check/r-devel-windows-x86_64/matrixStats-00check.html:

  Mingw-w64 runtime failure:
    VirtualProtect failed with code 0x5af
Running the tests in 'tests/rowRanges.R' failed.
Complete output:
  Error in gsub("([\\])", "\\\\\\1", expansion) :
    invalid regular expression '([\])', reason 'Out of memory'
  Calls: Sys.setenv ... .expand_R_libs_env_var -> expand -> sprintf -> gsub
  In addition: Warning message:
  In gsub("([\\])", "\\\\\\1", expansion) :
    TRE pattern compilation error 'Out of memory'
  Execution halted

The full log is:

using R version 4.3.0 beta (2023-04-07 r84200 ucrt)
using platform: x86_64-w64-mingw32 (64-bit)
R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
running under: Windows Server 2022 x64 (build 20348)
using session charset: UTF-8
checking for file 'matrixStats/DESCRIPTION' ... OK
this is package 'matrixStats' version '0.63.0'
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 whether package 'matrixStats' can be installed ... OK
used C compiler: 'gcc.exe (GCC) 12.2.0'
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 ... OK
checking R files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [0s] OK
checking whether the package can be loaded with stated dependencies ... [0s] OK
checking whether the package can be unloaded cleanly ... [0s] OK
checking whether the namespace can be loaded with stated dependencies ... [0s] OK
checking whether the namespace can be unloaded cleanly ... [0s] OK
checking loading without being on the library search path ... [0s] OK
checking startup messages can be suppressed ... [0s] OK
checking use of S3 registration ... 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 ... [10s] OK
checking Rd files ... [6s] 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 line endings in C/C++/Fortran sources/headers ... OK
checking pragmas in C/C++ headers and code ... OK
checking compiled code ... OK
checking installed files from 'inst/doc' ... OK
checking files in 'vignettes' ... OK
checking examples ... [4s] OK
checking for unstated dependencies in 'tests' ... OK
checking tests ... [270s] ERROR
  Running 'allocArray.R' [1s]
  Running 'allocMatrix.R' [1s]
  Running 'allocVector.R' [1s]
  Running 'anyMissing.R' [1s]
  Running 'anyMissing_subset.R' [1s]
  Running 'benchmark.R' [21s]
  Running 'binCounts.R' [0s]
  Running 'binCounts_subset.R' [1s]
  Running 'binMeans,binCounts.R' [0s]
  Running 'binMeans,binCounts_subset.R' [0s]
  Running 'count.R' [0s]
  Running 'count_subset.R' [0s]
  Running 'diff2.R' [1s]
  Running 'diff2_subset.R' [1s]
  Running 'indexByRow.R' [1s]
  Running 'logSumExp.R' [1s]
  Running 'logSumExp_subset.R' [1s]
  Running 'mean2.R' [1s]
  Running 'mean2_subset.R' [1s]
  Running 'product.R' [1s]
  Running 'product_subset.R' [1s]
  Running 'psortKM.R' [1s]
  Running 'rowAllAnys.R' [2s]
  Running 'rowAllAnys_subset.R' [22s]
  Running 'rowAvgsPerColSet.R' [1s]
  Running 'rowAvgsPerColSet_subset.R' [1s]
  Running 'rowCollapse.R' [1s]
  Running 'rowCollapse_subset.R' [1s]
  Running 'rowCounts.R' [1s]
  Running 'rowCounts_subset.R' [9s]
  Running 'rowCumMinMaxs.R' [1s]
  Running 'rowCumMinMaxs_subset.R' [8s]
  Running 'rowCumprods.R' [1s]
  Running 'rowCumprods_subset.R' [5s]
  Running 'rowCumsums.R' [1s]
  Running 'rowCumsums_subset.R' [4s]
  Running 'rowDiffs.R' [0s]
  Running 'rowDiffs_subset.R' [0s]
  Running 'rowIQRs.R' [0s]
  Running 'rowIQRs_subset.R' [4s]
  Running 'rowLogSumExps.R' [0s]
  Running 'rowLogSumExps_subset.R' [0s]
  Running 'rowMads.R' [1s]
  Running 'rowMads_subset.R' [3s]
  Running 'rowMeans2.R' [1s]
  Running 'rowMeans2_subset.R' [1s]
  Running 'rowMedians.R' [1s]
  Running 'rowMedians_subset.R' [2s]
  Running 'rowOrderStats.R' [1s]
  Running 'rowOrderStats_subset.R' [4s]
  Running 'rowProds.R' [1s]
  Running 'rowProds_subset.R' [4s]
  Running 'rowQuantiles.R' [65s]
  Running 'rowQuantiles_subset.R' [0s]
  Running 'rowRanges.R' [0s]
  Running 'rowRanges_subset.R' [3s]
  Running 'rowRanks.R' [11s]
  Running 'rowRanks_subset.R' [2s]
  Running 'rowSds.R' [0s]
  Running 'rowSds_subset.R' [2s]
  Running 'rowSums2.R' [1s]
  Running 'rowSums2_subset.R' [3s]
  Running 'rowTabulates.R' [1s]
  Running 'rowTabulates_subset.R' [5s]
  Running 'rowVarDiffs.R' [2s]
  Running 'rowVarDiffs_mad,iqr_subset.R' [11s]
  Running 'rowVarDiffs_var,sd_subset.R' [12s]
  Running 'rowVars.R' [0s]
  Running 'rowVars_subset.R' [3s]
  Running 'rowWeightedMeans.R' [1s]
  Running 'rowWeightedMeans_subset.R' [4s]
  Running 'rowWeightedMedians.R' [1s]
  Running 'rowWeightedMedians_subset.R' [4s]
  Running 'rowWeightedVars.R' [1s]
  Running 'rowWeightedVars_subset.R' [7s]
  Running 'signTabulate.R' [1s]
  Running 'signTabulate_subset.R' [1s]
  Running 'sum2.R' [1s]
  Running 'sum2_subset.R' [1s]
  Running 'validateIndices.R' [1s]
  Running 'varDiff_etal.R' [1s]
  Running 'varDiff_etal_subset.R' [2s]
  Running 'weightedMean.R' [1s]
  Running 'weightedMean_subset.R' [1s]
  Running 'weightedMedian.R' [1s]
  Running 'weightedMedian_subset.R' [1s]
  Running 'weightedVar.R' [1s]
  Running 'weightedVar_etal.R' [1s]
  Running 'weightedVar_etal_subset.R' [1s]
  Running 'x_OP_y.R' [0s]
  Running 'x_OP_y_subset.R' [0s]
  Running 'zzz.package-unload.R' [1s]
Running the tests in 'tests/rowDiffs.R' failed.
Complete output:

Running the tests in 'tests/rowDiffs_subset.R' failed.
Complete output:

Running the tests in 'tests/rowIQRs.R' failed.
Complete output:

Running the tests in 'tests/rowLogSumExps.R' failed.
Complete output:

Running the tests in 'tests/rowQuantiles_subset.R' failed.
Complete output:

  R version 4.3.0 beta (2023-04-07 r84200 ucrt) -- "Already Tomorrow"
  Copyright (C) 2023 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.

  Mingw-w64 runtime failure:
    VirtualProtect failed with code 0x5af
Running the tests in 'tests/rowRanges.R' failed.
Complete output:
  Error in gsub("([\\])", "\\\\\\1", expansion) :
    invalid regular expression '([\])', reason 'Out of memory'
  Calls: Sys.setenv ... .expand_R_libs_env_var -> expand -> sprintf -> gsub
  In addition: Warning message:
  In gsub("([\\])", "\\\\\\1", expansion) :
    TRE pattern compilation error 'Out of memory'
  Execution halted
Running the tests in 'tests/rowVars.R' failed.
Complete output:

Running the tests in 'tests/x_OP_y.R' failed.
Complete output:

Running the tests in 'tests/x_OP_y_subset.R' failed.
Complete output:

checking for unstated dependencies in vignettes ... OK
checking package vignettes in 'inst/doc' ... OK
checking re-building of vignette outputs ...
HenrikBengtsson commented 1 year ago

Yeah, it seems to have been a glitch. All OK again with using R version 4.3.0 beta (2023-04-09 r84208 ucrt)

Dianabeth3 commented 11 months ago

Good morning, how are you? I am running poolparty but in the PPstat module, I get the following error:

le$ bash PPstats pp_stats.config |& tee log.stats_example.txt ALERT: pp_stats.config has been specified as the configuration file [1] "R ALERT: Checking for R dependencies. Will attempt to install automatically if not present." CONF: Parameter check passed. moving on... CONF 1/8 Complete, summary acquired and proportion of genomic overlap detected CONF 2/8 Complete, total mean coverage calculated CONF 3/8 Complete, filtered mean coverage calculated CONF 4/8 Complete, proportion of ref genome calculated CONF 5/8 Complete, scaffold proportion calculated CONF 6/8 Complete, anchored proportion calculated CONF 7/8 Complete, interval proportion calculated CONF 8/8 Complete, chromosome proportion calculated CONF BASH portion of run is complete CONF Loading R to plot results and create tables [1] "R ALERT: Summary Written" Error in colMaxs(tma$Mean_Coverage) : could not find function "colMaxs" Execution halted CONF all files have been written to /home/ecolintegr/bin/poolparty/example/stats (poolparty_env) ecolintegr@ecolintegr-Precision-5820-Tower:~/bin/poolparty/example$

I installed the rpm package, but it does not generate the output pdf files. Could you help me or what should I do, I installed R 4.0.0.

Saludos, Diana