| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:37:46 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 825/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicFiles 1.39.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the GenomicFiles package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicFiles.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: GenomicFiles |
| Version: 1.39.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicFiles.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GenomicFiles_1.39.0.tar.gz |
| StartedAt: 2024-03-28 02:22:39 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 02:32:33 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 594.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GenomicFiles.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicFiles.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GenomicFiles_1.39.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/GenomicFiles.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GenomicFiles/DESCRIPTION' ... OK
* this is package 'GenomicFiles' version '1.39.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'MatrixGenerics', 'GenomicRanges',
'SummarizedExperiment', 'BiocParallel', 'Rsamtools', 'rtracklayer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'GenomicFiles' 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 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'S4Vectors:::selectSome'
See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
checkRd: (5) GenomicFiles-class.Rd:40-43: \item in \describe must have non-empty label
checkRd: (5) VcfStack-class.Rd:61-89: \item in \describe must have non-empty label
checkRd: (5) VcfStack-class.Rd:90-105: \item in \describe must have non-empty label
checkRd: (5) pack-methods.Rd:57-61: \item in \describe must have non-empty label
checkRd: (-1) reduceByFile-methods.Rd:132-139: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) reduceByFile-methods.Rd:140-143: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) reduceByRange-methods.Rd:143-150: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) reduceByRange-methods.Rd:151-154: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) registry-utils.Rd:45-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) registry-utils.Rd:60-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) registry-utils.Rd:64-68: 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'GenomicFiles-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VcfStack
> ### Title: VcfStack and RangedVcfStack Objects
> ### Aliases: class:VcfStack VcfStack-class RangedVcfStack-class VcfStack
> ### RangedVcfStack colnames,VcfStack-method rownames,VcfStack-method
> ### dimnames,VcfStack-method files,VcfStack-method
> ### files<-,VcfStack,character-method files<-,VcfStack,VcfFile-method
> ### files<-,VcfStack,VcfFileList-method seqinfo,VcfStack-method
> ### seqinfo<-,VcfStack-method seqinfo<-,RangedVcfStack-method
> ### seqlevelsStyle<-,VcfStack-method
> ### seqlevelsStyle<-,RangedVcfStack-method colData,VcfStack-method
> ### colData<-,VcfStack,DataFrame-method rowRanges,RangedVcfStack-method
> ### rowRanges<-,RangedVcfStack,GRanges-method vcfFields,VcfStack-method
> ### assay,VcfStack,ANY-method assay,RangedVcfStack,ANY-method
> ### readVcfStack show,VcfStack-method [,VcfStack,ANY,ANY-method
> ### [,VcfStack,ANY,ANY,ANY-method [,RangedVcfStack,ANY,ANY-method
> ### [,RangedVcfStack,ANY,ANY,ANY-method paths1kg dim,VcfStack-method
>
> ### ** Examples
>
> ## ---------------------------------------------------------------------
> ## CONSTRUCTION
> ## ---------------------------------------------------------------------
> ## point to VCF files and add names corresponding to the sequence
> ## present in the file
> extdata <- system.file(package="GenomicFiles", "extdata")
> files <- dir(extdata, pattern="^CEUtrio.*bgz$", full=TRUE)
> names(files) <- sub(".*_([0-9XY]+).*", "\\1", basename(files))
>
> ## input data.frame describing the length of each sequence, coerce to
> ## 'Seqinfo' object
> seqinfo <- as(readRDS(file.path(extdata, "seqinfo.rds")), "Seqinfo")
>
> stack <- VcfStack(files, seqinfo)
> stack
VcfStack object with 7 files and 3 samples
Seqinfo object with 25 sequences from hg19 genome
use 'readVcfStack()' to extract VariantAnnotation VCF.
>
> ## Use seqinfo from VCF files instead of explict value
> stack2 <- VcfStack(files)
>
> rstack <- RangedVcfStack(stack)
> gr <- GRanges(c("7:1-159138000", "X:1-155270560"))
> rstack2 <- RangedVcfStack(stack, gr)
> rstack2
VcfStack object with 7 files and 3 samples
GRanges object with 2 ranges and 0 metadata columns
Seqinfo object with 25 sequences from hg19 genome
use 'readVcfStack()' to extract VariantAnnotation VCF.
>
> ## ---------------------------------------------------------------------
> ## ACCESSORS
> ## ---------------------------------------------------------------------
> dim(stack)
[1] 7 3
> colnames(stack)
[1] "NA12878" "NA12891" "NA12892"
> rownames(stack)
[1] "11" "20" "21" "22" "7" "X" "Y"
> dimnames(stack)
[[1]]
[1] "11" "20" "21" "22" "7" "X" "Y"
[[2]]
[1] "NA12878" "NA12891" "NA12892"
> head(files(stack))
VcfFileList of length 6
names(6): 11 20 21 22 7 X
> seqinfo(stack)
Seqinfo object with 25 sequences from hg19 genome:
seqnames seqlengths isCircular genome
1 249250621 <NA> hg19
2 243199373 <NA> hg19
3 198022430 <NA> hg19
4 191154276 <NA> hg19
5 180915260 <NA> hg19
... ... ... ...
21 48129895 <NA> hg19
22 51304566 <NA> hg19
X 155270560 <NA> hg19
Y 59373566 <NA> hg19
MT 16569 <NA> hg19
> colData(stack)
DataFrame with 3 rows and 0 columns
>
> ## ---------------------------------------------------------------------
> ## METHODS
> ## ---------------------------------------------------------------------
> readVcfStack(stack, i=GRanges("20:862167-62858306"))
class: CollapsedVCF
dim: 317 3
rowRanges(vcf):
GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
info(vcf):
DataFrame with 26 columns: AC, AF, AN, BaseQRankSum, CCC, ClippingRankSum,...
info(header(vcf)):
Number Type Description
AC A Integer Allele count in genotypes, for each ALT al...
AF A Float Allele Frequency, for each ALT allele, in ...
AN 1 Integer Total number of alleles in called genotypes
BaseQRankSum 1 Float Z-score from Wilcoxon rank sum test of Alt...
CCC 1 Integer Number of called chromosomes
ClippingRankSum 1 Float Z-score From Wilcoxon rank sum test of Alt...
DB 0 Flag dbSNP Membership
DP 1 Integer Approximate read depth; some reads may hav...
DS 0 Flag Were any of the samples downsampled?
END 1 Integer Stop position of the interval
FS 1 Float Phred-scaled p-value using Fisher's exact ...
GQ_MEAN 1 Float Mean of all GQ values
GQ_STDDEV 1 Float Standard deviation of all GQ values
HWP 1 Float P value from test of Hardy Weinberg Equili...
HaplotypeScore 1 Float Consistency of the site with at most two s...
InbreedingCoeff 1 Float Inbreeding coefficient as estimated from t...
MLEAC A Integer Maximum likelihood expectation (MLE) for t...
MLEAF A Float Maximum likelihood expectation (MLE) for t...
MQ 1 Float RMS Mapping Quality
MQ0 1 Integer Total Mapping Quality Zero Reads
MQRankSum 1 Float Z-score From Wilcoxon rank sum test of Alt...
NCC 1 Integer Number of no-called samples
QD 1 Float Variant Confidence/Quality by Depth
ReadPosRankSum 1 Float Z-score from Wilcoxon rank sum test of Alt...
SOR 1 Float Symmetric Odds Ratio of 2x2 contingency ta...
set 1 String Source VCF for the merged record in Combin...
geno(vcf):
List of length 9: GT, AD, DP, GQ, MIN_DP, PGT, PID, PL, SB
geno(header(vcf)):
Number Type Description
GT 1 String Genotype
AD . Integer Allelic depths for the ref and alt alleles in the o...
DP 1 Integer Approximate read depth (reads with MQ=255 or with b...
GQ 1 Integer Genotype Quality
MIN_DP 1 Integer Minimum DP observed within the GVCF block
PGT 1 String Physical phasing haplotype information, describing ...
PID 1 String Physical phasing ID information, where each unique ...
PL G Integer Normalized, Phred-scaled likelihoods for genotypes ...
SB 4 Integer Per-sample component statistics which comprise the ...
> i <- GRanges(c("20:862167-62858306", "7:1-159138000"))
> readVcfStack(stack, i=i, j="NA12891")
class: CollapsedVCF
dim: 318 1
rowRanges(vcf):
GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
info(vcf):
DataFrame with 26 columns: AC, AF, AN, BaseQRankSum, CCC, ClippingRankSum,...
info(header(vcf)):
Number Type Description
AC A Integer Allele count in genotypes, for each ALT al...
AF A Float Allele Frequency, for each ALT allele, in ...
AN 1 Integer Total number of alleles in called genotypes
BaseQRankSum 1 Float Z-score from Wilcoxon rank sum test of Alt...
CCC 1 Integer Number of called chromosomes
ClippingRankSum 1 Float Z-score From Wilcoxon rank sum test of Alt...
DB 0 Flag dbSNP Membership
DP 1 Integer Approximate read depth; some reads may hav...
DS 0 Flag Were any of the samples downsampled?
END 1 Integer Stop position of the interval
FS 1 Float Phred-scaled p-value using Fisher's exact ...
GQ_MEAN 1 Float Mean of all GQ values
GQ_STDDEV 1 Float Standard deviation of all GQ values
HWP 1 Float P value from test of Hardy Weinberg Equili...
HaplotypeScore 1 Float Consistency of the site with at most two s...
InbreedingCoeff 1 Float Inbreeding coefficient as estimated from t...
MLEAC A Integer Maximum likelihood expectation (MLE) for t...
MLEAF A Float Maximum likelihood expectation (MLE) for t...
MQ 1 Float RMS Mapping Quality
MQ0 1 Integer Total Mapping Quality Zero Reads
MQRankSum 1 Float Z-score From Wilcoxon rank sum test of Alt...
NCC 1 Integer Number of no-called samples
QD 1 Float Variant Confidence/Quality by Depth
ReadPosRankSum 1 Float Z-score from Wilcoxon rank sum test of Alt...
SOR 1 Float Symmetric Odds Ratio of 2x2 contingency ta...
set 1 String Source VCF for the merged record in Combin...
geno(vcf):
List of length 9: GT, AD, DP, GQ, MIN_DP, PGT, PID, PL, SB
geno(header(vcf)):
Number Type Description
GT 1 String Genotype
AD . Integer Allelic depths for the ref and alt alleles in the o...
DP 1 Integer Approximate read depth (reads with MQ=255 or with b...
GQ 1 Integer Genotype Quality
MIN_DP 1 Integer Minimum DP observed within the GVCF block
PGT 1 String Physical phasing haplotype information, describing ...
PID 1 String Physical phasing ID information, where each unique ...
PL G Integer Normalized, Phred-scaled likelihoods for genotypes ...
SB 4 Integer Per-sample component statistics which comprise the ...
>
> head(assay(stack, gr))
non-single nucleotide variations are set to NA
Warning in .local(x, ...) : non-diploid variants are set to NA
NA12878 NA12891 NA12892
rs760352870 1 0 0
X:193438_G/C 2 2 NA
X:386831_A/G 2 NA NA
X:672818_T/C NA 2 NA
X:1784428_C/G 0 0 2
X:1861132_C/T 2 NA 0
> head(assay(rstack2))
Warning in socketConnection(port = port, server = TRUE, blocking = TRUE, :
port 11521 cannot be opened
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'head': cannot open the connection
Calls: head ... newSOCKnode -> socketConnection -> .handleSimpleError -> h
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'GenomicFiles_unit_tests.R'
OK
* 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, 2 NOTEs
See
'F:/biocbuild/bbs-3.19-bioc/meat/GenomicFiles.Rcheck/00check.log'
for details.
GenomicFiles.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL GenomicFiles ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'GenomicFiles' ... ** using staged installation ** R ** 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 (GenomicFiles)
GenomicFiles.Rcheck/tests/GenomicFiles_unit_tests.Rout
R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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.
> BiocGenerics:::testPackage("GenomicFiles")
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
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
RUNIT TEST PROTOCOL -- Thu Mar 28 02:32:22 2024
***********************************************
Number of test functions: 20
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomicFiles RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20
Number of errors: 0
Number of failures: 0
Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 1 out-of-bound range located on sequence 19.
Note that ranges located on a sequence whose length is unknown (NA) or
on a circular sequence are not considered out-of-bound (use
seqlengths() and isCircular() to get the lengths and circularity flags
of the underlying sequences). You can use trim() to trim these ranges.
See ?`trim,GenomicRanges-method` for more information.
>
> proc.time()
user system elapsed
61.85 1.42 247.79
GenomicFiles.Rcheck/GenomicFiles-Ex.timings
| name | user | system | elapsed | |
| GenomicFiles-class | 4.11 | 0.03 | 38.22 | |