Gregory Ryslik
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/SpacePAC |
| Branch: RELEASE_3_9 |
| Last Commit: 0bfdf2b |
| Last Changed Date: 2019-05-02 11:53:44 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:03:09 -0400 (Wed, 16 Oct 2019).
| Package 1556/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SpacePAC 1.22.0 Gregory Ryslik
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: SpacePAC |
| Version: 1.22.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SpacePAC.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SpacePAC_1.22.0.tar.gz |
| StartedAt: 2019-10-16 05:10:24 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:13:03 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 159.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpacePAC.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SpacePAC.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SpacePAC_1.22.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SpacePAC.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpacePAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpacePAC’ version ‘1.22.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpacePAC’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Package in Depends field not imported from: ‘iPAC’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SpaceClust: no visible global function definition for ‘flush.console’
SpaceClust: no visible global function definition for ‘ppois’
create.Distance.Matrix: no visible global function definition for
‘dist’
create.Result.Matrix: no visible global function definition for
‘p.adjust’
get.Avg.Neighbor.Distance: no visible global function definition for
‘dist’
get.Local.Radius.Results: no visible global function definition for
‘sd’
make.3D.Sphere: no visible global function definition for ‘rgl.open’
make.3D.Sphere: no visible global function definition for ‘rgl.bg’
make.3D.Sphere: no visible global function definition for ‘plot3d’
make.3D.Sphere: no visible global function definition for ‘decorate3d’
make.3D.Sphere: no visible global function definition for ‘spheres3d’
Undefined global functions or variables:
decorate3d dist flush.console p.adjust plot3d ppois rgl.bg rgl.open
sd spheres3d
Consider adding
importFrom("stats", "dist", "p.adjust", "ppois", "sd")
importFrom("utils", "flush.console")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SpaceClust 52.029 0.179 52.933
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/SpacePAC.Rcheck/00check.log’
for details.
SpacePAC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SpacePAC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘SpacePAC’ ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SpacePAC)
SpacePAC.Rcheck/tests/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.
> BiocGenerics:::testPackage("SpacePAC")
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
Attaching package: 'gdata'
The following object is masked from 'package:stats':
nobs
The following object is masked from 'package:utils':
object.size
The following object is masked from 'package:base':
startsWith
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from 'package:gdata':
combine
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, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:gdata':
first, first<-
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:gdata':
trim
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Processing radius # 1 : radius length = 1.00 : Percentage complete 0.00
Processing radius # 2 : radius length = 2.00 : Percentage complete 0.25
Processing radius # 3 : radius length = 3.00 : Percentage complete 0.50
Processing radius # 4 : radius length = 4.00 : Percentage complete 0.75
Processing radius # 1 : radius length = 1.00 : Percentage complete 0.00
Processing radius # 2 : radius length = 2.00 : Percentage complete 0.25
Processing radius # 3 : radius length = 3.00 : Percentage complete 0.50
Processing radius # 4 : radius length = 4.00 : Percentage complete 0.75
RUNIT TEST PROTOCOL -- Wed Oct 16 05:13:00 2019
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
SpacePAC RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
16.177 0.208 16.378
SpacePAC.Rcheck/SpacePAC-Ex.timings
| name | user | system | elapsed | |
| SpaceClust | 52.029 | 0.179 | 52.933 | |
| SpacePAC-package | 0.001 | 0.000 | 0.001 | |
| make.3D.Sphere | 0.001 | 0.000 | 0.000 | |