Luyi Tian
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/scPipe |
| Branch: RELEASE_3_7 |
| Last Commit: 19a1726 |
| Last Changed Date: 2018-05-31 19:42:56 -0400 (Thu, 31 May 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:30:51 -0400 (Wed, 17 Oct 2018).
| Package 1332/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| scPipe 1.2.1 Luyi Tian
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: scPipe |
| Version: 1.2.1 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:scPipe.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings scPipe_1.2.1.tar.gz |
| StartedAt: 2018-10-16 03:37:36 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 03:40:39 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 183.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scPipe.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:scPipe.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings scPipe_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/scPipe.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scPipe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scPipe’ version ‘1.2.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘scPipe’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
libs 5.2Mb
* 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
* 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 ... NOTE
plot_demultiplex: no visible binding for global variable ‘status’
plot_demultiplex: no visible binding for global variable ‘count’
plot_demultiplex: no visible binding for global variable ‘label_y’
plot_demultiplex: no visible binding for global variable ‘label_tx’
Undefined global functions or variables:
count label_tx label_y status
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sc_sample_data 6.788 0.004 6.793
plot_QC_pairs 6.704 0.012 6.725
calculate_QC_metrics 0.816 0.036 8.943
get_genes_by_GO 0.224 0.004 7.906
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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
‘/home/biocbuild/bbs-3.7-bioc/meat/scPipe.Rcheck/00check.log’
for details.
scPipe.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL scPipe
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘scPipe’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c Gene.cpp -o Gene.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c Interval.cpp -o Interval.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c cellbarcode.cpp -o cellbarcode.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c detect_barcode.cpp -o detect_barcode.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c parsebam.cpp -o parsebam.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c parsecount.cpp -o parsecount.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c transcriptmapping.cpp -o transcriptmapping.o
transcriptmapping.cpp: In member function ‘void Mapping::parse_align(std::__cxx11::string, std::__cxx11::string, bool, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int, int)’:
transcriptmapping.cpp:605:30: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(of, header);
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c trimbarcode.cpp -o trimbarcode.o
trimbarcode.cpp: In function ‘void paired_fastq_to_bam(char*, char*, char*, read_s, filter_s)’:
trimbarcode.cpp:92:27: warning: ignoring return value of ‘int sam_hdr_write(samFile*, const bam_hdr_t*)’, declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(fp, hdr);
^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include -fpic -g -O2 -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o scPipe.so Gene.o Interval.o RcppExports.o cellbarcode.o detect_barcode.o parsebam.o parsecount.o rcpp_scPipe_func.o transcriptmapping.o trimbarcode.o utils.o -L/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/usrlib -Wl,-rpath,/home/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/usrlib -lhts -lz -lm -lbz2 -llzma -lpthread -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/scPipe/libs
** R
** data
** 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
* DONE (scPipe)
scPipe.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(scPipe)
Loading required package: ggplot2
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply
>
> test_check("scPipe")
[1] "organism/gene_id_type not provided. Make a guess: mmusculus_gene_ensembl / ensembl_gene_id"
══ testthat results ═══════════════════════════════════════════════════════════
OK: 14 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
7.384 0.256 7.650
scPipe.Rcheck/scPipe-Ex.timings
| name | user | system | elapsed | |
| QC_metrics | 0.676 | 0.000 | 0.675 | |
| UMI_dup_info | 0.112 | 0.004 | 0.115 | |
| UMI_duplication | 0.072 | 0.004 | 0.075 | |
| calculate_QC_metrics | 0.816 | 0.036 | 8.943 | |
| cell_barcode_matching | 0.068 | 0.004 | 0.069 | |
| convert_geneid | 0.380 | 0.008 | 4.632 | |
| create_processed_report | 0.000 | 0.000 | 0.001 | |
| create_report | 0.000 | 0.000 | 0.001 | |
| create_sce_by_dir | 0.068 | 0.000 | 0.068 | |
| demultiplex_info | 0.068 | 0.000 | 0.068 | |
| detect_outlier | 0.192 | 0.000 | 0.196 | |
| gene_id_type | 0.064 | 0.000 | 0.064 | |
| get_genes_by_GO | 0.224 | 0.004 | 7.906 | |
| organism | 0.088 | 0.000 | 0.087 | |
| plot_QC_pairs | 6.704 | 0.012 | 6.725 | |
| plot_UMI_dup | 0.236 | 0.000 | 0.237 | |
| plot_demultiplex | 0.224 | 0.004 | 0.226 | |
| plot_mapping | 0.584 | 0.000 | 0.586 | |
| remove_outliers | 0.204 | 0.000 | 0.207 | |
| sc_count_aligned_bam | 0.000 | 0.000 | 0.001 | |
| sc_demultiplex | 0.000 | 0.000 | 0.002 | |
| sc_demultiplex_and_count | 0 | 0 | 0 | |
| sc_detect_bc | 0.000 | 0.000 | 0.001 | |
| sc_exon_mapping | 0.004 | 0.000 | 0.001 | |
| sc_gene_counting | 0.000 | 0.000 | 0.001 | |
| sc_sample_data | 6.788 | 0.004 | 6.793 | |
| sc_sample_qc | 0.556 | 0.000 | 0.555 | |
| sc_trim_barcode | 0.000 | 0.000 | 0.001 | |