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) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:53:29 -0400 (Tue, 16 Apr 2019).
| Package 209/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ccfindR 1.2.1 Jun Woo
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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 |
##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################
* 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.
ccfindR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ccfindR ### ############################################################################## ############################################################################## * 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)
ccfindR.Rcheck/ccfindR-Ex.timings
| name | user | system | elapsed | |
| basis-set-scNMFSet-method | 0.364 | 0.028 | 0.393 | |
| basis-set | 0.268 | 0.032 | 0.301 | |
| basis | 0.160 | 0.012 | 0.172 | |
| build_tree | 3.716 | 0.008 | 3.727 | |
| cell_map | 0.528 | 0.000 | 0.528 | |
| cluster_id | 3.888 | 0.000 | 3.893 | |
| coeff-set-scNMFSet-method | 0.072 | 0.000 | 0.074 | |
| coeff-set | 0.092 | 0.000 | 0.093 | |
| coeff | 0.156 | 0.000 | 0.153 | |
| colData-scNMFSet-method | 0.160 | 0.000 | 0.162 | |
| colData-set-scNMFSet-ANY-method | 0.116 | 0.000 | 0.113 | |
| counts-scNMFSet-method | 0.052 | 0.000 | 0.052 | |
| counts-set-scNMFSet-method | 0.092 | 0.012 | 0.104 | |
| factorize | 8.360 | 0.032 | 8.412 | |
| feature_map | 0.276 | 0.000 | 0.284 | |
| filter_cells | 0.084 | 0.000 | 0.080 | |
| filter_genes | 0.112 | 0.000 | 0.114 | |
| gene_map | 0.276 | 0.000 | 0.273 | |
| measure-set-scNMFSet-method | 0.080 | 0.000 | 0.081 | |
| measure-set | 0.104 | 0.000 | 0.104 | |
| measure | 0.148 | 0.000 | 0.146 | |
| meta_genes | 0.364 | 0.000 | 0.364 | |
| normalize_count | 0.084 | 0.000 | 0.082 | |
| optimal_rank | 3.608 | 0.000 | 3.634 | |
| plot_genes | 0.060 | 0.000 | 0.059 | |
| plot_tree | 2.832 | 0.008 | 2.843 | |
| ranks-set-scNMFSet-method | 0.108 | 0.000 | 0.107 | |
| ranks-set | 0.092 | 0.000 | 0.093 | |
| ranks | 0.084 | 0.000 | 0.083 | |
| read_10x | 0.200 | 0.000 | 0.198 | |
| remove_zeros | 0.068 | 0.000 | 0.070 | |
| rename_tips | 2.596 | 0.016 | 2.611 | |
| rowData-scNMFSet-method | 0.048 | 0.000 | 0.049 | |
| scNMFSet-class | 0.188 | 0.000 | 0.188 | |
| scNMFSet | 0.048 | 0.000 | 0.050 | |
| show-scNMFSet-method | 0.048 | 0.000 | 0.051 | |
| simulate_data | 0.052 | 0.000 | 0.054 | |
| simulate_whx | 2.752 | 0.000 | 2.751 | |
| vb_factorize | 3.252 | 0.000 | 3.261 | |
| visualize_clusters | 1.220 | 0.000 | 1.232 | |
| write_10x | 0.060 | 0.000 | 0.057 | |