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CHECK report for ccfindR on malbec1

This page was generated on 2019-04-16 11:53:29 -0400 (Tue, 16 Apr 2019).

Package 209/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ccfindR 1.2.1
Jun Woo
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/ccfindR
Branch: RELEASE_3_8
Last Commit: b13e377
Last Changed Date: 2019-01-03 13:45:27 -0400 (Thu, 03 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ccfindR
Version: 1.2.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ccfindR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ccfindR_1.2.1.tar.gz
StartedAt: 2019-04-15 22:42:28 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:45:24 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 176.7 seconds
RetCode: 0
Status:  OK 
CheckDir: ccfindR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ccfindR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ccfindR_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/ccfindR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ccfindR/DESCRIPTION’ ... OK
* this is package ‘ccfindR’ version ‘1.2.1’
* 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 ‘ccfindR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
* 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
--------------------------------------------------------------------------
[[19800,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:

Module: OpenFabrics (openib)
  Host: malbec1

Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
feature_map: no visible binding for global variable ‘sd’
show,scNMFSet: no visible global function definition for ‘head’
Undefined global functions or variables:
  head sd
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "head")
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 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
factorize 8.36  0.032   8.412
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/ccfindR.Rcheck/00check.log’
for details.



Installation output

ccfindR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ccfindR
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘ccfindR’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c vbnmf_update.cpp -o vbnmf_update.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o ccfindR.so RcppExports.o vbnmf_update.o -lgsl -lgslcblas -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/ccfindR/libs
** 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
* DONE (ccfindR)

Tests output


Example timings

ccfindR.Rcheck/ccfindR-Ex.timings

nameusersystemelapsed
basis-set-scNMFSet-method0.3640.0280.393
basis-set0.2680.0320.301
basis0.1600.0120.172
build_tree3.7160.0083.727
cell_map0.5280.0000.528
cluster_id3.8880.0003.893
coeff-set-scNMFSet-method0.0720.0000.074
coeff-set0.0920.0000.093
coeff0.1560.0000.153
colData-scNMFSet-method0.1600.0000.162
colData-set-scNMFSet-ANY-method0.1160.0000.113
counts-scNMFSet-method0.0520.0000.052
counts-set-scNMFSet-method0.0920.0120.104
factorize8.3600.0328.412
feature_map0.2760.0000.284
filter_cells0.0840.0000.080
filter_genes0.1120.0000.114
gene_map0.2760.0000.273
measure-set-scNMFSet-method0.0800.0000.081
measure-set0.1040.0000.104
measure0.1480.0000.146
meta_genes0.3640.0000.364
normalize_count0.0840.0000.082
optimal_rank3.6080.0003.634
plot_genes0.0600.0000.059
plot_tree2.8320.0082.843
ranks-set-scNMFSet-method0.1080.0000.107
ranks-set0.0920.0000.093
ranks0.0840.0000.083
read_10x0.2000.0000.198
remove_zeros0.0680.0000.070
rename_tips2.5960.0162.611
rowData-scNMFSet-method0.0480.0000.049
scNMFSet-class0.1880.0000.188
scNMFSet0.0480.0000.050
show-scNMFSet-method0.0480.0000.051
simulate_data0.0520.0000.054
simulate_whx2.7520.0002.751
vb_factorize3.2520.0003.261
visualize_clusters1.2200.0001.232
write_10x0.0600.0000.057