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This page was generated on 2022-04-13 12:06:53 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 midasHLA on tokay2


To the developers/maintainers of the midasHLA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/midasHLA.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.

raw results

Package 1148/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
midasHLA 1.2.0  (landing page)
Maciej MigdaƂ
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/midasHLA
git_branch: RELEASE_3_14
git_last_commit: 811d9d5
git_last_commit_date: 2021-10-26 13:07:22 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: midasHLA
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:midasHLA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings midasHLA_1.2.0.tar.gz
StartedAt: 2022-04-12 22:52:38 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 23:00:30 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 472.0 seconds
RetCode: 0
Status:   OK  
CheckDir: midasHLA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:midasHLA.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings midasHLA_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/midasHLA.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'midasHLA/DESCRIPTION' ... OK
* this is package 'midasHLA' version '1.2.0'
* 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 'midasHLA' can be installed ... OK
* 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
* 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 ... 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 ... NOTE
  Note: found 1180 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
runMiDAS     13.08   0.10   13.19
kableResults  6.55   0.08    6.62
omnibusTest   5.17   0.27    5.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
runMiDAS         12.60   0.03   12.63
kableResults      7.41   0.04    7.47
getAAFrequencies  5.37   0.16    5.53
omnibusTest       5.41   0.09    5.50
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/midasHLA.Rcheck/00check.log'
for details.



Installation output

midasHLA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/midasHLA_1.2.0.tar.gz && rm -rf midasHLA.buildbin-libdir && mkdir midasHLA.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=midasHLA.buildbin-libdir midasHLA_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL midasHLA_1.2.0.zip && rm midasHLA_1.2.0.tar.gz midasHLA_1.2.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 39 1724k   39  677k    0     0  1008k      0  0:00:01 --:--:--  0:00:01 1008k
100 1724k  100 1724k    0     0  1279k      0  0:00:01  0:00:01 --:--:-- 1279k

install for i386

* installing *source* package 'midasHLA' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'midasHLA'
    finding HTML links ... done
    HWETest                                 html  
    LRTest                                  html  
    MiDAS-class                             html  
    finding level-2 HTML links ... done

    MiDAS_tut_HLA                           html  
    MiDAS_tut_KIR                           html  
    MiDAS_tut_object                        html  
    MiDAS_tut_pheno                         html  
    aaVariationToCounts                     html  
    adjustPValues                           html  
    allele_frequencies                      html  
    analyzeAssociations                     html  
    analyzeConditionalAssociations          html  
    applyInheritanceModel                   html  
    as.data.frame.MiDAS                     html  
    backquote                               html  
    characterMatches                        html  
    checkAlleleFormat                       html  
    checkColDataFormat                      html  
    checkHlaCallsFormat                     html  
    checkKirCallsFormat                     html  
    checkKirGenesFormat                     html  
    checkStatisticalModel                   html  
    colnamesMatches                         html  
    convertAlleleToVariable                 html  
    countsToVariables                       html  
    dfToExperimentMat                       html  
    dict_dist_grantham                      html  
    distGrantham                            html  
    experimentMatToDf                       html  
    filterByFrequency                       html  
    filterByOmnibusGroups                   html  
    filterByVariables                       html  
    filterExperimentByFrequency             html  
    filterExperimentByVariables             html  
    filterListByElements                    html  
    formatResults                           html  
    getAAFrequencies                        html  
    getAlleleResolution                     html  
    getAllelesForAA                         html  
    getExperimentFrequencies                html  
    getExperimentPopulationMultiplicator    html  
    getExperiments                          html  
    getFrequencies                          html  
    getFrequencyMask                        html  
    getHlaCalls                             html  
    getHlaCallsGenes                        html  
    getHlaFrequencies                       html  
    getHlaKirInteractions                   html  
    getKIRFrequencies                       html  
    getKirCalls                             html  
    getObjectDetails                        html  
    getOmnibusGroups                        html  
    getPlaceholder                          html  
    getReferenceFrequencies                 html  
    getVariableAAPos                        html  
    hasTidyMethod                           html  
    hlaAlignmentGrantham                    html  
    hlaCallsGranthamDistance                html  
    hlaCallsToCounts                        html  
    hlaToAAVariation                        html  
    hlaToVariable                           html  
    isCharacterOrNULL                       html  
    isClass                                 html  
    isClassOrNULL                           html  
    isCountOrNULL                           html  
    isCountsOrZeros                         html  
    isExperimentCountsOrZeros               html  
    isExperimentInheritanceModelApplicable
                                            html  
    isFlagOrNULL                            html  
    isNumberOrNULL                          html  
    isStringOrNULL                          html  
    isTRUEorFALSE                           html  
    iterativeLRT                            html  
    iterativeModel                          html  
    kableResults                            html  
    kir_frequencies                         html  
    lapply_tryCatch                         html  
    listMiDASDictionaries                   html  
    midasToWide                             html  
    objectHasPlaceholder                    html  
    omnibusTest                             html  
    prepareMiDAS                            html  
    prepareMiDAS_hla_NK_ligands             html  
    prepareMiDAS_hla_aa                     html  
    prepareMiDAS_hla_alleles                html  
    prepareMiDAS_hla_custom                 html  
    prepareMiDAS_hla_divergence             html  
    prepareMiDAS_hla_g_groups               html  
    prepareMiDAS_hla_het                    html  
    prepareMiDAS_hla_kir_interactions       html  
    prepareMiDAS_hla_supertypes             html  
    prepareMiDAS_kir_custom                 html  
    prepareMiDAS_kir_genes                  html  
    prepareMiDAS_kir_haplotypes             html  
    readHlaAlignments                       html  
    readHlaCalls                            html  
    readKirCalls                            html  
    reduceAlleleResolution                  html  
    reduceHlaCalls                          html  
    runMiDAS                                html  
    runMiDASGetVarsFreq                     html  
    stringMatches                           html  
    summariseAAPosition                     html  
    updateModel                             html  
    validateFrequencyCutoffs                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'midasHLA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'midasHLA' as midasHLA_1.2.0.zip
* DONE (midasHLA)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'midasHLA' successfully unpacked and MD5 sums checked

Tests output

midasHLA.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(midasHLA)
Loading required package: MultiAssayExperiment
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, 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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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

> 
> test_check("midasHLA")
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 309 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 309 ]
> 
> proc.time()
   user  system elapsed 
  63.06    2.00   65.35 

midasHLA.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(midasHLA)
Loading required package: MultiAssayExperiment
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, 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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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

> 
> test_check("midasHLA")
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 309 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 309 ]
> 
> proc.time()
   user  system elapsed 
  64.78    1.26   66.18 

Example timings

midasHLA.Rcheck/examples_i386/midasHLA-Ex.timings

nameusersystemelapsed
HWETest1.770.071.83
analyzeAssociations0.560.010.58
analyzeConditionalAssociations0.540.020.56
checkAlleleFormat000
checkKirGenesFormat000
convertAlleleToVariable0.000.000.06
countsToVariables0.050.000.04
filterByFrequency0.460.010.49
filterByOmnibusGroups0.190.000.19
filterByVariables0.410.100.50
formatResults000
getAAFrequencies4.780.154.98
getAlleleResolution000
getAllelesForAA0.810.020.83
getExperiments000
getFrequencies0.240.040.27
getHlaCalls0.060.010.08
getHlaFrequencies0.150.000.15
getHlaKirInteractions3.520.173.82
getKIRFrequencies000
getKirCalls0.030.030.06
getOmnibusGroups0.020.000.01
getPlaceholder000
getVariableAAPos0.010.020.04
hlaCallsGranthamDistance1.160.021.17
hlaToAAVariation3.080.293.37
hlaToVariable0.290.000.30
kableResults6.550.086.62
omnibusTest5.170.275.44
prepareMiDAS0.410.010.42
readHlaAlignments0.580.000.58
readHlaCalls0.150.000.17
readKirCalls0.110.020.16
reduceAlleleResolution000
reduceHlaCalls0.330.010.34
runMiDAS13.08 0.1013.19
summariseAAPosition0.660.000.66

midasHLA.Rcheck/examples_x64/midasHLA-Ex.timings

nameusersystemelapsed
HWETest1.950.041.98
analyzeAssociations0.820.000.81
analyzeConditionalAssociations0.620.000.63
checkAlleleFormat000
checkKirGenesFormat000
convertAlleleToVariable000
countsToVariables0.000.030.03
filterByFrequency0.340.010.36
filterByOmnibusGroups0.170.000.18
filterByVariables0.460.000.45
formatResults000
getAAFrequencies5.370.165.53
getAlleleResolution000
getAllelesForAA1.480.031.52
getExperiments000
getFrequencies0.300.020.31
getHlaCalls0.050.030.08
getHlaFrequencies0.760.020.78
getHlaKirInteractions2.430.112.53
getKIRFrequencies000
getKirCalls0.040.010.07
getOmnibusGroups0.020.000.01
getPlaceholder000
getVariableAAPos0.010.000.02
hlaCallsGranthamDistance1.180.031.20
hlaToAAVariation3.570.143.72
hlaToVariable0.460.000.45
kableResults7.410.047.47
omnibusTest5.410.095.50
prepareMiDAS0.320.000.33
readHlaAlignments0.490.020.50
readHlaCalls0.140.000.14
readKirCalls0.030.010.04
reduceAlleleResolution000
reduceHlaCalls0.180.020.20
runMiDAS12.60 0.0312.63
summariseAAPosition0.540.010.56