Maciej Migdał
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/midasHLA |
| git_branch: RELEASE_3_13 |
| git_last_commit: 9e6b7ff |
| git_last_commit_date: 2021-05-19 13:00:15 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:11 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1132/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| midasHLA 1.0.0 (landing page) Maciej Migdał
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: midasHLA |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:midasHLA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings midasHLA_1.0.0.tar.gz |
| StartedAt: 2021-10-15 01:55:22 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 02:05:12 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 589.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: midasHLA.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:midasHLA.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings midasHLA_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/midasHLA.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.0.0'
* 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 25.60 0.43 26.06
omnibusTest 16.42 0.27 16.68
getAAFrequencies 14.23 0.27 14.73
hlaToAAVariation 10.62 0.27 10.89
kableResults 5.97 0.17 6.14
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runMiDAS 22.38 0.26 22.68
omnibusTest 15.12 0.58 15.70
hlaToAAVariation 11.95 0.55 12.50
getAAFrequencies 12.07 0.42 12.48
kableResults 8.08 0.03 8.11
* 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-3.13-bioc/meat/midasHLA.Rcheck/00check.log'
for details.
midasHLA.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/midasHLA_1.0.0.tar.gz && rm -rf midasHLA.buildbin-libdir && mkdir midasHLA.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=midasHLA.buildbin-libdir midasHLA_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL midasHLA_1.0.0.zip && rm midasHLA_1.0.0.tar.gz midasHLA_1.0.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 1648k 0 15987 0 0 132k 0 0:00:12 --:--:-- 0:00:12 132k
72 1648k 72 1192k 0 0 1052k 0 0:00:01 0:00:01 --:--:-- 1052k
100 1648k 100 1648k 0 0 1208k 0 0:00:01 0:00:01 --:--:-- 1207k
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_1.0.0.zip
* DONE (midasHLA)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'midasHLA' successfully unpacked and MD5 sums checked
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midasHLA.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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(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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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 311 ]
>
> proc.time()
user system elapsed
83.73 3.15 87.17
|
midasHLA.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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(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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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 311 ]
>
> proc.time()
user system elapsed
83.10 2.00 85.12
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midasHLA.Rcheck/examples_i386/midasHLA-Ex.timings
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midasHLA.Rcheck/examples_x64/midasHLA-Ex.timings
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