| Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-20 11:32:15 -0400 (Mon, 20 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
| 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 | ||||
| Package 1231/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| midasHLA 1.13.0 (landing page) Maciej Migdał
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
|
To the developers/maintainers of the midasHLA package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: midasHLA |
| Version: 1.13.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:midasHLA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings midasHLA_1.13.0.tar.gz |
| StartedAt: 2024-05-19 19:07:59 -0400 (Sun, 19 May 2024) |
| EndedAt: 2024-05-19 19:13:57 -0400 (Sun, 19 May 2024) |
| EllapsedTime: 357.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: midasHLA.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:midasHLA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings midasHLA_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/midasHLA.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘midasHLA/DESCRIPTION’ ... OK
* this is package ‘midasHLA’ version ‘1.13.0’
* 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 for sufficient/correct file permissions ... 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 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 ... NOTE
checkRd: (-1) omnibusTest.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) omnibusTest.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) omnibusTest.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) omnibusTest.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) omnibusTest.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) omnibusTest.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) omnibusTest.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) runMiDAS.Rd:151-154: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runMiDAS.Rd:155-158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runMiDAS.Rd:159-163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runMiDAS.Rd:164-168: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'kableResults.Rd':
kableResults
Code: function(results, colnames = NULL, header = "MiDAS analysis
results", pvalue_cutoff = NULL, format = "html",
scroll_box_height = "400px")
Docs: function(results, colnames = NULL, header = "MiDAS analysis
results", pvalue_cutoff = NULL, format =
getOption("knitr.table.format"), scroll_box_height =
"400px")
Mismatches in argument default values:
Name: 'format' Code: "html" Docs: getOption("knitr.table.format")
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runMiDAS 11.602 0.264 11.914
omnibusTest 6.866 0.158 7.069
getAAFrequencies 5.412 0.160 5.627
kableResults 5.095 0.092 5.187
* 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:
anyMissing, rowMedians
>
> test_check("midasHLA")
[ FAIL 1 | WARN 20 | SKIP 0 | PASS 308 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_utils.R:166:3'): LRTest ──────────────────────────────────────
`lrt_res` not equal to data.frame(...).
Component "logLik": Mean relative difference: 0.005254902
Component "statistic": Mean relative difference: 0.005254902
[ FAIL 1 | WARN 20 | SKIP 0 | PASS 308 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/midasHLA.Rcheck/00check.log’
for details.
midasHLA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL midasHLA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * 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 ** 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 * DONE (midasHLA)
midasHLA.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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, 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, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
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
>
> test_check("midasHLA")
[ FAIL 1 | WARN 20 | SKIP 0 | PASS 308 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_utils.R:166:3'): LRTest ──────────────────────────────────────
`lrt_res` not equal to data.frame(...).
Component "logLik": Mean relative difference: 0.005254902
Component "statistic": Mean relative difference: 0.005254902
[ FAIL 1 | WARN 20 | SKIP 0 | PASS 308 ]
Error: Test failures
Execution halted
midasHLA.Rcheck/midasHLA-Ex.timings
| name | user | system | elapsed | |
| HWETest | 1.087 | 0.031 | 1.117 | |
| analyzeAssociations | 0.531 | 0.007 | 0.539 | |
| analyzeConditionalAssociations | 1.160 | 0.009 | 1.170 | |
| checkAlleleFormat | 0 | 0 | 0 | |
| checkKirGenesFormat | 0 | 0 | 0 | |
| convertAlleleToVariable | 0.005 | 0.001 | 0.006 | |
| countsToVariables | 0.019 | 0.032 | 0.052 | |
| filterByFrequency | 0.164 | 0.013 | 0.177 | |
| filterByOmnibusGroups | 0.061 | 0.002 | 0.063 | |
| filterByVariables | 0.176 | 0.004 | 0.179 | |
| formatResults | 0.000 | 0.000 | 0.001 | |
| getAAFrequencies | 5.412 | 0.160 | 5.627 | |
| getAlleleResolution | 0.000 | 0.000 | 0.001 | |
| getAllelesForAA | 1.625 | 0.022 | 1.647 | |
| getExperiments | 0.001 | 0.001 | 0.000 | |
| getFrequencies | 0.243 | 0.049 | 0.292 | |
| getHlaCalls | 0.093 | 0.085 | 0.179 | |
| getHlaFrequencies | 0.174 | 0.026 | 0.200 | |
| getHlaKirInteractions | 2.266 | 0.230 | 2.507 | |
| getKIRFrequencies | 0.005 | 0.000 | 0.006 | |
| getKirCalls | 0.031 | 0.074 | 0.107 | |
| getOmnibusGroups | 0.014 | 0.012 | 0.026 | |
| getPlaceholder | 0 | 0 | 0 | |
| getVariableAAPos | 0.018 | 0.001 | 0.020 | |
| hlaCallsGranthamDistance | 1.198 | 0.096 | 1.294 | |
| hlaToAAVariation | 3.818 | 0.568 | 4.435 | |
| hlaToVariable | 0.281 | 0.029 | 0.315 | |
| kableResults | 5.095 | 0.092 | 5.187 | |
| omnibusTest | 6.866 | 0.158 | 7.069 | |
| prepareMiDAS | 0.250 | 0.012 | 0.262 | |
| readHlaAlignments | 1.471 | 0.019 | 1.491 | |
| readHlaCalls | 0.129 | 0.004 | 0.133 | |
| readKirCalls | 0.039 | 0.129 | 0.168 | |
| reduceAlleleResolution | 0.001 | 0.000 | 0.001 | |
| reduceHlaCalls | 0.218 | 0.143 | 0.361 | |
| runMiDAS | 11.602 | 0.264 | 11.914 | |
| summariseAAPosition | 0.688 | 0.005 | 0.694 | |