Gregory Ryslik
| Snapshot Date: 2019-10-14 17:00:44 -0400 (Mon, 14 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 2019-10-15 13:02:22 -0400 (Tue, 15 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 | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SpacePAC |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpacePAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SpacePAC_1.22.0.tar.gz |
| StartedAt: 2019-10-15 07:15:38 -0400 (Tue, 15 Oct 2019) |
| EndedAt: 2019-10-15 07:20:05 -0400 (Tue, 15 Oct 2019) |
| EllapsedTime: 267.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpacePAC.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpacePAC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SpacePAC_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SpacePAC.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SpaceClust 42.02 0.74 43.27
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SpaceClust 47.64 0.78 48.72
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.9-bioc/meat/SpacePAC.Rcheck/00check.log'
for details.
SpacePAC.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SpacePAC_1.22.0.tar.gz && rm -rf SpacePAC.buildbin-libdir && mkdir SpacePAC.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SpacePAC.buildbin-libdir SpacePAC_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SpacePAC_1.22.0.zip && rm SpacePAC_1.22.0.tar.gz SpacePAC_1.22.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 782k 100 782k 0 0 12.9M 0 --:--:-- --:--:-- --:--:-- 14.6M
install for i386
* installing *source* package 'SpacePAC' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SpacePAC'
finding HTML links ... done
SpaceClust html
SpacePAC-package html
make.3D.Sphere html
** 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
install for x64
* installing *source* package 'SpacePAC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SpacePAC' as SpacePAC_1.22.0.zip
* DONE (SpacePAC)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SpacePAC' successfully unpacked and MD5 sums checked
|
SpacePAC.Rcheck/tests_i386/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
The following object is masked from 'package:grDevices':
windows
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 -- Tue Oct 15 07:19:40 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
16.45 0.43 17.53
|
SpacePAC.Rcheck/tests_x64/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-w64-mingw32/x64 (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
The following object is masked from 'package:grDevices':
windows
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 -- Tue Oct 15 07:19:55 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
13.06 0.31 14.01
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SpacePAC.Rcheck/examples_i386/SpacePAC-Ex.timings
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SpacePAC.Rcheck/examples_x64/SpacePAC-Ex.timings
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