Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:05:04 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 CellBarcode on nebbiolo2


To the developers/maintainers of the CellBarcode package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CellBarcode.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 267/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellBarcode 1.3.0  (landing page)
Wenjie Sun
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/CellBarcode
git_branch: master
git_last_commit: 0ec7508
git_last_commit_date: 2022-04-26 12:19:50 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CellBarcode
Version: 1.3.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:CellBarcode.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings CellBarcode_1.3.0.tar.gz
StartedAt: 2022-06-23 19:04:47 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 19:08:24 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 216.9 seconds
RetCode: 0
Status:   OK  
CheckDir: CellBarcode.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:CellBarcode.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings CellBarcode_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/CellBarcode.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellBarcode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellBarcode’ version ‘1.3.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CellBarcode’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bc_2matrix,BarcodeObj: no visible binding for global variable
  ‘barcode_seq’
bc_cure_depth,BarcodeObj : <anonymous>: no visible binding for global
  variable ‘barcode_seq’
bc_cure_umi,BarcodeObj : <anonymous>: no visible binding for global
  variable ‘barcode_seq’
bc_cure_umi,BarcodeObj : <anonymous>: no visible binding for global
  variable ‘umi_seq’
bc_extract,character: no visible binding for global variable ‘i’
bc_plot_seqQc,BarcodeQcSet: no visible binding for global variable
  ‘sample_name’
bc_subset,BarcodeObj : <anonymous>: no visible binding for global
  variable ‘barcode_seq’
Undefined global functions or variables:
  barcode_seq i sample_name umi_seq
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/CellBarcode.Rcheck/00check.log’
for details.



Installation output

CellBarcode.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL CellBarcode
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘CellBarcode’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c lib.cpp -o lib.o
lib.cpp: In function ‘int hamm_dist(std::string, std::string)’:
lib.cpp:59:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   59 |     for (int i=0; i < s1.length(); i++) {
      |                   ~~^~~~~~~~~~~~~
lib.cpp: In function ‘Rcpp::List seq_correct(std::vector<std::__cxx11::basic_string<char> >, Rcpp::IntegerVector, int, int, int, int, int, int)’:
lib.cpp:123:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  123 |     for (auto i=0; i<seq.size(); i++) {
      |                    ~^~~~~~~~~~~
lib.cpp:159:18: warning: variable ‘flag_is_connetcted’ set but not used [-Wunused-but-set-variable]
  159 |             bool flag_is_connetcted = false;
      |                  ^~~~~~~~~~~~~~~~~~
lib.cpp:230:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<std::__cxx11::basic_string<char>, int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  230 |     for (auto i=0; i<res.size(); i++) {
      |                    ~^~~~~~~~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o CellBarcode.so RcppExports.o lib.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/library/00LOCK-CellBarcode/00new/CellBarcode/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 (CellBarcode)

Tests output

CellBarcode.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics"
Copyright (C) 2022 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(CellBarcode)
> 
> test_check("CellBarcode")
------------
bc_cure_depth: isUpdate is FALSE, use messyBc as input.
------------
------------
+.BarcodeObj: You are merge data with UMI to data without UMI. The UMI info are discarded.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is FALSE, use messyBc as input.
------------
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, 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: BiocParallel
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: Rsamtools
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
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: 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

------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 35 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 35 ]
> 
> proc.time()
   user  system elapsed 
 12.356   1.244  13.480 

Example timings

CellBarcode.Rcheck/CellBarcode-Ex.timings

nameusersystemelapsed
BarcodeObj0.5720.0250.574
bc_2df0.0250.0000.017
bc_auto_cutoff0.0040.0000.003
bc_barcodes0.0010.0000.001
bc_cleanBc0.0040.0000.005
bc_cure_cluster0.1530.0040.145
bc_cure_depth0.0280.0000.018
bc_cure_umi0.0200.0000.012
bc_extract0.3340.0070.335
bc_messyBc0.0040.0000.005
bc_meta0.0040.0000.004
bc_names0.0000.0010.001
bc_plot_mutual1.0120.0781.090
bc_plot_pair0.1570.0040.161
bc_plot_single0.3900.0240.414
bc_seq_filter0.3430.0270.369
bc_seq_qc1.2090.0241.233
bc_subset0.1190.0000.100
bc_summary_barcode0.3900.0000.382
bc_summary_seqQc2.4530.0202.474
format0.0030.0000.003
show0.0030.0000.003
sub-BarcodeQcSet-ANY-ANY-ANY-method2.6160.1162.732