| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:07:24 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
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To the developers/maintainers of the SpatialDecon package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpatialDecon.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1846/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpatialDecon 1.4.3 (landing page) Nicole Ortogero
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SpatialDecon |
| Version: 1.4.3 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpatialDecon.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SpatialDecon_1.4.3.tar.gz |
| StartedAt: 2022-04-13 03:20:05 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 03:52:43 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 1957.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpatialDecon.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SpatialDecon.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings SpatialDecon_1.4.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/SpatialDecon.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SpatialDecon/DESCRIPTION' ... OK
* this is package 'SpatialDecon' version '1.4.3'
* package encoding: UTF-8
* 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 'SpatialDecon' can be installed ... OK
* 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
download_profile_matrix: no visible binding for global variable
'profile_matrix'
Undefined global functions or variables:
profile_matrix
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runCollapseCellTypes-NanoStringGeoMxSet-method 102.36 0.47 102.84
runReverseDecon 96.19 0.10 96.30
runReverseDecon-NanoStringGeoMxSet-method 94.73 0.24 94.96
runCollapseCellTypes 91.14 0.14 91.28
runspatialdecon 75.41 1.08 76.57
runspatialdecon-Seurat-method 48.43 1.51 50.59
runspatialdecon-NanoStringGeoMxSet-method 22.24 0.10 22.33
runMergeTumorIntoX-NanoStringGeoMxSet-method 13.88 0.06 13.94
runMergeTumorIntoX 13.87 0.05 13.92
runErrorModel 13.43 0.03 13.47
reverseDecon 9.39 0.01 9.41
spatialdecon 7.33 0.02 7.34
SpatialDecon-package 6.70 0.12 6.83
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runReverseDecon-NanoStringGeoMxSet-method 117.39 0.05 117.44
runReverseDecon 116.47 0.08 116.55
runCollapseCellTypes-NanoStringGeoMxSet-method 111.49 0.07 111.58
runCollapseCellTypes 110.71 0.03 110.74
runspatialdecon 64.20 0.74 65.00
runspatialdecon-Seurat-method 46.19 0.73 47.47
runspatialdecon-NanoStringGeoMxSet-method 24.53 0.06 24.59
runMergeTumorIntoX 20.15 0.03 20.19
runMergeTumorIntoX-NanoStringGeoMxSet-method 18.19 0.00 18.18
runErrorModel 15.32 0.05 15.37
reverseDecon 9.72 0.00 9.72
SpatialDecon-package 7.36 0.06 7.42
spatialdecon 6.75 0.00 6.75
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/SpatialDecon.Rcheck/00check.log'
for details.
SpatialDecon.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/SpatialDecon_1.4.3.tar.gz && rm -rf SpatialDecon.buildbin-libdir && mkdir SpatialDecon.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SpatialDecon.buildbin-libdir SpatialDecon_1.4.3.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL SpatialDecon_1.4.3.zip && rm SpatialDecon_1.4.3.tar.gz SpatialDecon_1.4.3.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
18 3957k 18 728k 0 0 1139k 0 0:00:03 --:--:-- 0:00:03 1138k
64 3957k 64 2564k 0 0 1555k 0 0:00:02 0:00:01 0:00:01 1555k
100 3957k 100 3957k 0 0 1833k 0 0:00:02 0:00:02 --:--:-- 1833k
install for i386
* installing *source* package 'SpatialDecon' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SpatialDecon'
finding HTML links ... done
SpatialDecon-package html
TIL_barplot html
cellcols html
collapseCellTypes html
create_profile_matrix html
derive_GeoMx_background html
download_profile_matrix html
florets html
mean.resid.sd html
mergeTumorIntoX html
mini_geomx_dataset html
mini_singleCell_dataset html
nsclc html
reverseDecon html
runCollapseCellTypes-NanoStringGeoMxSet-method
html
runCollapseCellTypes html
runErrorModel html
runMergeTumorIntoX-NanoStringGeoMxSet-method
html
runMergeTumorIntoX html
runReverseDecon-NanoStringGeoMxSet-method
html
runReverseDecon html
runspatialdecon-NanoStringGeoMxSet-method
html
runspatialdecon-Seurat-method html
runspatialdecon html
safeTME html
safeTME.matches html
spatialdecon 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 'SpatialDecon' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SpatialDecon' as SpatialDecon_1.4.3.zip
* DONE (SpatialDecon)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'SpatialDecon' successfully unpacked and MD5 sums checked
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SpatialDecon.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> library(testthat)
> library(SpatialDecon)
>
> test_check("SpatialDecon")
[1] "Creating Atlas"
[1] "1 / 4 : B"
[1] "2 / 4 : C"
[1] "3 / 4 : A"
[1] "4 / 4 : D"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 85 ]
>
> proc.time()
user system elapsed
213.68 0.90 215.79
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SpatialDecon.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> library(testthat)
> library(SpatialDecon)
>
> test_check("SpatialDecon")
[1] "Creating Atlas"
[1] "1 / 4 : B"
[1] "2 / 4 : C"
[1] "3 / 4 : A"
[1] "4 / 4 : D"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 85 ]
>
> proc.time()
user system elapsed
243.62 0.79 251.18
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SpatialDecon.Rcheck/examples_i386/SpatialDecon-Ex.timings
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SpatialDecon.Rcheck/examples_x64/SpatialDecon-Ex.timings
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