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This page was generated on 2022-12-03 11:10:03 -0500 (Sat, 03 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4277
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4152
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
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

CHECK results for scPipe on merida1


To the developers/maintainers of the scPipe package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scPipe.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1794/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scPipe 1.21.1  (landing page)
Luyi Tian
Snapshot Date: 2022-12-02 14:00:12 -0500 (Fri, 02 Dec 2022)
git_url: https://git.bioconductor.org/packages/scPipe
git_branch: master
git_last_commit: 51fb1de
git_last_commit_date: 2022-11-10 02:03:29 -0500 (Thu, 10 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'SingleCellExperiment' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is not available

Summary

Package: scPipe
Version: 1.21.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scPipe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scPipe_1.21.1.tar.gz
StartedAt: 2022-12-03 06:07:01 -0500 (Sat, 03 Dec 2022)
EndedAt: 2022-12-03 06:18:07 -0500 (Sat, 03 Dec 2022)
EllapsedTime: 666.1 seconds
RetCode: 0
Status:   OK  
CheckDir: scPipe.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scPipe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scPipe_1.21.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/scPipe.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.21.1’
* 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 ... 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
* 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
Namespace in Imports field not imported from: ‘scater’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
anno_to_saf: no visible binding for global variable ‘GeneID’
convert_geneid: no visible global function definition for ‘useMart’
get_genes_by_GO: no visible global function definition for ‘useMart’
infer_gene_id_from_parent: no visible binding for global variable
  ‘type’
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:
  GeneID count label_tx label_y status type useMart
* 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library/scPipe/libs/scPipe.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
sc_sample_data       12.703  0.093  17.963
plot_QC_pairs        12.471  0.122  17.051
anno_import           5.081  0.179   7.755
calculate_QC_metrics  4.137  0.374   6.566
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/scPipe.Rcheck/00check.log’
for details.



Installation output

scPipe.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scPipe
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘scPipe’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/testthat/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c Gene.cpp -o Gene.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/testthat/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c Interval.cpp -o Interval.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/testthat/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/testthat/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c cellbarcode.cpp -o cellbarcode.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/testthat/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c detect_barcode.cpp -o detect_barcode.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/testthat/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c parsebam.cpp -o parsebam.o
parsebam.cpp:116:9: warning: unused variable 'map_status' [-Wunused-variable]
    int map_status;
        ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/testthat/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c parsecount.cpp -o parsecount.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/testthat/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c rcpp_scPipe_func.cpp -o rcpp_scPipe_func.o
In file included from rcpp_scPipe_func.cpp:3:
./trimbarcode.h:11:1: warning: unused function 'kseq_init' [-Wunused-function]
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include/htslib/kseq.h:240:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include/htslib/kseq.h:237:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_BASIC(SCOPE, type_t)                                     \
        ^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include/htslib/kseq.h:165:16: note: expanded from macro '__KSEQ_BASIC'
        SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
                      ^
In file included from rcpp_scPipe_func.cpp:3:
./trimbarcode.h:11:1: warning: unused function 'kseq_destroy' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include/htslib/kseq.h:240:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include/htslib/kseq.h:237:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_BASIC(SCOPE, type_t)                                     \
        ^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include/htslib/kseq.h:171:13: note: expanded from macro '__KSEQ_BASIC'
        SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
                   ^
In file included from rcpp_scPipe_func.cpp:3:
./trimbarcode.h:11:1: warning: unused function 'kseq_read' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include/htslib/kseq.h:240:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include/htslib/kseq.h:238:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_READ(SCOPE)
        ^
/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include/htslib/kseq.h:185:12: note: expanded from macro '__KSEQ_READ'
        SCOPE int kseq_read(kseq_t *seq) \
                  ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/testthat/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c test-cpp.cpp -o test-cpp.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/testthat/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c test-runner.cpp -o test-runner.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/testthat/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c transcriptmapping.cpp -o transcriptmapping.o
transcriptmapping.cpp:701:20: warning: unused variable 'bam_hdr' [-Wunused-variable]
        bam_hdr_t *bam_hdr = bam_hdr_read(fp);
                   ^
transcriptmapping.cpp:699:25: warning: unused function 'get_bc_umi_lengths' [-Wunused-function]
    std::pair<int, int> get_bc_umi_lengths(string bam_fn) {
                        ^
In file included from transcriptmapping.cpp:2:
./transcriptmapping.h:140:15: warning: private field 'SOURCE' is not used [-Wunused-private-field]
    const int SOURCE     = 1;
              ^
./transcriptmapping.h:144:15: warning: private field 'SCORE' is not used [-Wunused-private-field]
    const int SCORE      = 5;
              ^
./transcriptmapping.h:146:15: warning: private field 'PHASE' is not used [-Wunused-private-field]
    const int PHASE      = 7;
              ^
5 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/testthat/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c trimbarcode.cpp -o trimbarcode.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/testthat/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c utils.cpp -o utils.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 test-cpp.o test-runner.o transcriptmapping.o trimbarcode.o utils.o /Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3/Resources/library/00LOCK-scPipe/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scPipe)

Tests output

scPipe.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: 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, 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
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("scPipe")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 29 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 29 ]
> 
> proc.time()
   user  system elapsed 
 33.474   1.310  50.299 

Example timings

scPipe.Rcheck/scPipe-Ex.timings

nameusersystemelapsed
QC_metrics1.4700.0152.135
UMI_dup_info0.4460.0070.633
UMI_duplication0.4110.0110.603
anno_import5.0810.1797.755
anno_to_saf0.0000.0000.001
calculate_QC_metrics4.1370.3746.566
cell_barcode_matching0.4510.0530.712
convert_geneid0.9820.1031.539
create_processed_report000
create_report0.0000.0010.000
create_sce_by_dir0.4890.0300.740
demultiplex_info0.4690.0070.680
detect_outlier0.7210.0101.009
gene_id_type0.4310.0080.571
get_ercc_anno0.0010.0000.000
get_genes_by_GO1.4380.2082.408
get_read_str0.0010.0010.001
organism0.4310.0080.585
plot_QC_pairs12.471 0.12217.051
plot_UMI_dup1.0150.0181.330
plot_demultiplex0.8080.0101.096
plot_mapping1.8780.0402.734
remove_outliers0.8040.0081.112
sc_correct_bam_bc0.0010.0000.002
sc_count_aligned_bam000
sc_demultiplex0.0010.0000.002
sc_demultiplex_and_count000
sc_detect_bc000
sc_exon_mapping0.0020.0000.002
sc_gene_counting0.0010.0000.002
sc_sample_data12.703 0.09317.963
sc_sample_qc1.8060.0192.694
sc_trim_barcode000