Package: CellMapper

Version: 1.8.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:CellMapper.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings CellMapper_1.8.0.tar.gz

StartedAt: 2019-04-15 22:44:24 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:47:50 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 205.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CellMapper.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:CellMapper.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings CellMapper_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/CellMapper.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 ‘CellMapper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellMapper’ version ‘1.8.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CellMapper’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘stats::sd’ by ‘S4Vectors::sd’ when loading ‘CellMapper’
  Warning: replacing previous import ‘stats::var’ by ‘S4Vectors::var’ when loading ‘CellMapper’
See ‘/home/biocbuild/bbs-3.8-bioc/meat/CellMapper.Rcheck/00install.out’ for details.
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ReplicateManuscript 157.36  9.732 168.874
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/CellMapper.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL CellMapper
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘CellMapper’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘stats::sd’ by ‘S4Vectors::sd’ when loading ‘CellMapper’
Warning: replacing previous import ‘stats::var’ by ‘S4Vectors::var’ when loading ‘CellMapper’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘stats::sd’ by ‘S4Vectors::sd’ when loading ‘CellMapper’
Warning: replacing previous import ‘stats::var’ by ‘S4Vectors::var’ when loading ‘CellMapper’
* DONE (CellMapper)

name	user	system	elapsed
CMprep	0.132	0.008	0.141
CMsearch	0.152	0.000	0.153
CellMapperList-class	0.208	0.000	0.206
ExampleGeneLists	0.024	0.000	0.024
ReplicateManuscript	157.360	9.732	168.874