Zhe Wang
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/scruff |
| git_branch: RELEASE_3_13 |
| git_last_commit: 027572f |
| git_last_commit_date: 2021-05-19 12:36:52 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:22 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the scruff package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scruff.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 1716/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scruff 1.10.0 (landing page) Zhe Wang
| 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: scruff |
| Version: 1.10.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scruff.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings scruff_1.10.0.tar.gz |
| StartedAt: 2021-10-15 05:22:12 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 05:32:07 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 594.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scruff.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:scruff.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings scruff_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/scruff.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 'scruff/DESCRIPTION' ... OK
* this is package 'scruff' version '1.10.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'scruff' 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 ... NOTE
Unexported object imported by a ':::' call: 'ShortRead:::.set_omp_threads'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.Call(ShortRead:::.set_omp_threads, ...)
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
.countUmiUnit: no visible global function definition for '.'
.countUmiUnit: no visible binding for global variable 'gene_id'
.countUmiUnit: no visible binding for global variable 'umi'
.countUmiUnit: no visible binding for global variable 'inferred_umi'
.countUmiUnit: no visible global function definition for 'median'
.demultiplexUnit: no visible binding for global variable 'experiment'
.demultiplexUnit: no visible binding for global variable 'lane'
.demultiplexUnit: no visible binding for global variable 'filename'
.demultiplexUnit: no visible binding for global variable 'project'
.demultiplexUnit: no visible binding for global variable 'cell_index'
.demultiplexUnit: no visible binding for global variable 'reads'
.demultiplexUnit: no visible binding for global variable
'percent_assigned'
.demultiplexUnit: no visible binding for global variable 'read1_path'
.demultiplexUnit: no visible binding for global variable 'read2_path'
.demultiplexUnit: no visible binding for global variable 'min.phred1'
.demultiplexUnit: no visible binding for global variable 'length1'
.demultiplexUnit: no visible binding for global variable 'bc_correct'
.demultiplexUnit: no visible binding for global variable 'barcode'
.demultiplexUnit: no visible binding for global variable 'read2'
.demultiplexUnit: no visible binding for global variable 'qtring2'
.demultiplexUnit: no visible binding for global variable 'rname2'
.demultiplexUnit: no visible binding for global variable 'umi'
.demultiplexUnit: no visible binding for global variable 'fastq_path'
.demultiplexUnit: no visible binding for global variable 'read1'
.demultiplexUnit: no visible binding for global variable 'qtring1'
.demultiplexUnit: no visible binding for global variable 'rname1'
.getGeneAnnotation: no visible binding for global variable 'type'
.getGeneAnnotation: no visible binding for global variable 'gene_id'
.getGeneAnnotation: no visible binding for global variable 'gene_name'
.getGeneAnnotation: no visible binding for global variable
'gene_biotype'
.plotAvgReadsPerCorrectedUMI: no visible binding for global variable
'avg_reads_per_corrected_umi'
.plotAvgReadsPerCorrectedUMI: no visible binding for global variable
'experiment'
.plotAvgReadsPerCorrectedUMI: no visible binding for global variable
'number_of_cells'
.plotAvgReadsPerCorrectedUMI: no visible binding for global variable
'.x'
.plotAvgReadsPerUMI: no visible binding for global variable
'experiment'
.plotAvgReadsPerUMI: no visible binding for global variable
'avg_reads_per_umi'
.plotAvgReadsPerUMI: no visible binding for global variable
'number_of_cells'
.plotAvgReadsPerUMI: no visible binding for global variable '.x'
.plotCounts: no visible binding for global variable 'experiment'
.plotCounts: no visible binding for global variable 'total_counts'
.plotCounts: no visible binding for global variable 'number_of_cells'
.plotCounts: no visible binding for global variable '.x'
.plotFracProteinCodingGenes: no visible binding for global variable
'experiment'
.plotFracProteinCodingGenes: no visible binding for global variable
'protein_coding_genes'
.plotFracProteinCodingGenes: no visible binding for global variable
'number_of_cells'
.plotFracProteinCodingTranscripts: no visible binding for global
variable 'experiment'
.plotFracProteinCodingTranscripts: no visible binding for global
variable 'protein_coding_counts'
.plotFracProteinCodingTranscripts: no visible binding for global
variable 'total_counts'
.plotFracProteinCodingTranscripts: no visible binding for global
variable 'number_of_cells'
.plotGeneToGenomeFraction: no visible binding for global variable
'experiment'
.plotGeneToGenomeFraction: no visible binding for global variable
'reads_mapped_to_genes'
.plotGeneToGenomeFraction: no visible binding for global variable
'reads_mapped_to_genome'
.plotGeneToGenomeFraction: no visible binding for global variable
'number_of_cells'
.plotGeneToTotalFraction: no visible binding for global variable
'experiment'
.plotGeneToTotalFraction: no visible binding for global variable
'reads_mapped_to_genes'
.plotGeneToTotalFraction: no visible binding for global variable
'reads'
.plotGeneToTotalFraction: no visible binding for global variable
'number_of_cells'
.plotGenes: no visible binding for global variable 'experiment'
.plotGenes: no visible binding for global variable 'number_of_cells'
.plotGenes: no visible binding for global variable '.x'
.plotGenesPerMillionReads: no visible binding for global variable
'experiment'
.plotGenesPerMillionReads: no visible binding for global variable
'reads'
.plotGenesPerMillionReads: no visible binding for global variable
'number_of_cells'
.plotGenesPerMillionReads: no visible binding for global variable '.x'
.plotGenomeReadsFraction: no visible binding for global variable
'experiment'
.plotGenomeReadsFraction: no visible binding for global variable
'reads_mapped_to_genome'
.plotGenomeReadsFraction: no visible binding for global variable
'reads'
.plotGenomeReadsFraction: no visible binding for global variable
'number_of_cells'
.plotMedReadsPerCorrectedUMI: no visible binding for global variable
'median_reads_per_corrected_umi'
.plotMedReadsPerCorrectedUMI: no visible binding for global variable
'experiment'
.plotMedReadsPerCorrectedUMI: no visible binding for global variable
'number_of_cells'
.plotMedReadsPerCorrectedUMI: no visible binding for global variable
'.x'
.plotMedReadsPerUMI: no visible binding for global variable
'experiment'
.plotMedReadsPerUMI: no visible binding for global variable
'median_reads_per_umi'
.plotMedReadsPerUMI: no visible binding for global variable
'number_of_cells'
.plotMedReadsPerUMI: no visible binding for global variable '.x'
.plotMtCounts: no visible binding for global variable 'experiment'
.plotMtCounts: no visible binding for global variable 'mt_counts'
.plotMtCounts: no visible binding for global variable 'number_of_cells'
.plotMtCounts: no visible binding for global variable '.x'
.plotMtCountsFraction: no visible binding for global variable
'experiment'
.plotMtCountsFraction: no visible binding for global variable
'mt_counts'
.plotMtCountsFraction: no visible binding for global variable
'total_counts'
.plotMtCountsFraction: no visible binding for global variable
'number_of_cells'
.plotReadsMappedToGenes: no visible binding for global variable
'experiment'
.plotReadsMappedToGenes: no visible binding for global variable
'reads_mapped_to_genes'
.plotReadsMappedToGenes: no visible binding for global variable
'number_of_cells'
.plotReadsMappedToGenes: no visible binding for global variable '.x'
.plotReadsMappedToGenome: no visible binding for global variable
'experiment'
.plotReadsMappedToGenome: no visible binding for global variable
'reads_mapped_to_genome'
.plotReadsMappedToGenome: no visible binding for global variable
'number_of_cells'
.plotReadsMappedToGenome: no visible binding for global variable '.x'
.plotTotalReads: no visible binding for global variable 'experiment'
.plotTotalReads: no visible binding for global variable 'reads'
.plotTotalReads: no visible binding for global variable
'number_of_cells'
.plotTotalReads: no visible binding for global variable '.x'
.tenxBamqcUnit: no visible binding for global variable 'CB'
.tenxBamqcUnit: no visible global function definition for '.'
.tenxBamqcUnit: no visible binding for global variable 'readname'
.tenxBamqcUnit: no visible binding for global variable 'NH'
.tenxBamqcUnit: no visible binding for global variable 'GX'
.tenxBamqcUnit: no visible binding for global variable 'MM'
.tenxBamqcUnit: no visible binding for global variable 'cell_barcode'
.tenxBamqcUnit: no visible binding for global variable
'reads_mapped_to_genome'
.tenxBamqcUnit: no visible binding for global variable
'reads_mapped_to_genes'
.tenxCheckCellBarcodes: no visible binding for global variable
'cbtop10000'
.tenxCheckCellBarcodes: no visible binding for global variable
'v2chemistry'
.tenxCheckCellBarcodes: no visible global function definition for
'complete.cases'
.tenxCheckCellBarcodes: no visible binding for global variable
'v1chemistry'
.tenxCheckCellBarcodes: no visible binding for global variable
'v3chemistry'
alignRsubread: no visible global function definition for
'capture.output'
countUMI: no visible binding for global variable 'geneid'
countUMI: no visible binding for global variable 'gene_id'
countUMI: no visible binding for global variable 'gene_biotype'
demultiplex: no visible binding for global variable 'cell_index'
demultiplex: no visible binding for global variable 'filename'
gview : .getLevel: no visible binding for global variable 'level'
gview : .getTxdt: no visible binding for global variable
'transcript_id'
gview : .getTxdt: no visible binding for global variable
'transcript_name'
gview : .getTxdt: no visible binding for global variable 'gene_id'
gview : .getTxdt: no visible binding for global variable 'gene_name'
gview : .transRect: no visible binding for global variable
'transcript_id'
gview : .transRect: no visible binding for global variable 'level'
gview : .transRect: no visible binding for global variable 'type'
gview : .transRect: no visible binding for global variable
'exon_number'
gview : .transRect: no visible binding for global variable 'gene_id'
gview : .transRect: no visible binding for global variable 'gene_name'
gview : .transArrow: no visible binding for global variable 'level'
gview : .transArrow: no visible binding for global variable
'transcript_id'
gview : .transArrow: no visible binding for global variable
'transcript_name'
gview : .transArrow: no visible binding for global variable 'gene_id'
gview : .transArrow: no visible binding for global variable 'gene_name'
gview : .transText: no visible binding for global variable 'level'
gview : .transText: no visible binding for global variable
'transcript_name'
gview: no visible binding for global variable 'type'
gview: no visible binding for global variable 'x1'
gview: no visible binding for global variable 'x2'
gview: no visible binding for global variable 'y1'
gview: no visible binding for global variable 'y2'
gview: no visible binding for global variable 'x'
gview: no visible binding for global variable 'y'
gview: no visible binding for global variable 'transcript_name'
tenxBamqc: no visible binding for global variable 'cbtop10000'
tenxBamqc: no visible binding for global variable
'reads_mapped_to_genome'
tenxBamqc: no visible binding for global variable
'reads_mapped_to_genes'
tenxBamqc: no visible binding for global variable 'cb'
tenxBamqc: no visible binding for global variable 'cell_barcode'
tenxBamqc: no visible binding for global variable 'number_of_cells'
Undefined global functions or variables:
. .x CB GX MM NH avg_reads_per_corrected_umi avg_reads_per_umi
barcode bc_correct capture.output cb cbtop10000 cell_barcode
cell_index complete.cases exon_number experiment fastq_path filename
gene_biotype gene_id gene_name geneid inferred_umi lane length1 level
median median_reads_per_corrected_umi median_reads_per_umi min.phred1
mt_counts number_of_cells percent_assigned project
protein_coding_counts protein_coding_genes qtring1 qtring2 read1
read1_path read2 read2_path readname reads reads_mapped_to_genes
reads_mapped_to_genome rname1 rname2 total_counts transcript_id
transcript_name type umi v1chemistry v2chemistry v3chemistry x x1 x2
y y1 y2
Consider adding
importFrom("stats", "complete.cases", "median")
importFrom("utils", "capture.output")
to your NAMESPACE file.
* 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 ... 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
tenxBamqc 5.42 0.31 48.01
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
tenxBamqc 5.03 0.5 45.68
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/scruff.Rcheck/00check.log'
for details.
scruff.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/scruff_1.10.0.tar.gz && rm -rf scruff.buildbin-libdir && mkdir scruff.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scruff.buildbin-libdir scruff_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL scruff_1.10.0.zip && rm scruff_1.10.0.tar.gz scruff_1.10.0.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
28 4408k 28 1247k 0 0 1867k 0 0:00:02 --:--:-- 0:00:02 1867k
100 4408k 100 4408k 0 0 2991k 0 0:00:01 0:00:01 --:--:-- 2993k
install for i386
* installing *source* package 'scruff' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'scruff'
finding HTML links ... done
alignRsubread html
bamExample html
barcodeExample html
cbtop10000 html
countUMI html
demultiplex html
gview html
qcplots html
rview html
sceExample html
scruff html
tenxBamqc html
validCb 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 'scruff' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scruff' as scruff_1.10.0.zip
* DONE (scruff)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'scruff' successfully unpacked and MD5 sums checked
|
scruff.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(scruff)
>
> test_check("scruff")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
14.54 1.46 15.98
|
scruff.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(scruff)
>
> test_check("scruff")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
>
> proc.time()
user system elapsed
16.50 0.73 17.21
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scruff.Rcheck/examples_i386/scruff-Ex.timings
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scruff.Rcheck/examples_x64/scruff-Ex.timings
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