| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:59 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the BloodGen3Module package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BloodGen3Module.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 201/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BloodGen3Module 1.0.0 (landing page) Darawan Rinchai
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: BloodGen3Module |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BloodGen3Module.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BloodGen3Module_1.0.0.tar.gz |
| StartedAt: 2021-10-14 20:22:36 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 20:30:39 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 483.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BloodGen3Module.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BloodGen3Module.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BloodGen3Module_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BloodGen3Module.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BloodGen3Module/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BloodGen3Module' version '1.0.0'
* 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 'BloodGen3Module' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module'
Warning: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module'
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BloodGen3Module.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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... 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 R/sysdata.rda ... 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
Groupcomparison 22.07 2.02 25.33
gridplot 18.72 0.19 19.36
fingerprintplot 11.32 0.46 12.39
Individualcomparison 10.49 0.51 11.58
Groupcomparisonlimma 10.68 0.19 11.52
fold_change 4.81 0.09 5.48
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Groupcomparison 22.20 1.29 24.63
gridplot 18.14 0.25 18.88
fingerprintplot 11.60 0.26 12.48
Groupcomparisonlimma 10.89 0.26 11.72
Individualcomparison 9.29 0.27 10.22
fold_change 4.91 0.11 5.59
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-fold_change.R'
OK
** running tests for arch 'x64' ...
Running 'test-fold_change.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 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/BloodGen3Module.Rcheck/00check.log'
for details.
BloodGen3Module.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BloodGen3Module_1.0.0.tar.gz && rm -rf BloodGen3Module.buildbin-libdir && mkdir BloodGen3Module.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BloodGen3Module.buildbin-libdir BloodGen3Module_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BloodGen3Module_1.0.0.zip && rm BloodGen3Module_1.0.0.tar.gz BloodGen3Module_1.0.0.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
1 170k 1 2487 0 0 19843 0 0:00:08 --:--:-- 0:00:08 19896
100 170k 100 170k 0 0 626k 0 --:--:-- --:--:-- --:--:-- 626k
install for i386
* installing *source* package 'BloodGen3Module' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module'
Warning: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module'
** help
*** installing help indices
converting help for package 'BloodGen3Module'
finding HTML links ... done
Gen3_ann html
Groupcomparison html
Groupcomparisonlimma html
Individualcomparison html
Module_listGen3 html
color html
fingerprintplot html
fold_change html
gridplot html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module'
Warning: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module'
Warning: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'BloodGen3Module' ...
** testing if installed package can be loaded
Warning: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module'
Warning: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module'
Warning: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module'
* MD5 sums
packaged installation of 'BloodGen3Module' as BloodGen3Module_1.0.0.zip
* DONE (BloodGen3Module)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BloodGen3Module' successfully unpacked and MD5 sums checked
|
BloodGen3Module.Rcheck/tests_i386/test-fold_change.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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("gtools")
> library("testthat")
> library("BloodGen3Module")
Warning messages:
1: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module'
2: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module'
3: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module'
4: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module'
>
> fold_change = function(df_raw = df_raw,
+ sample_info = sample_info,
+ Group_column = Group_column,
+ Test_group=Test_group,
+ Ref_group=Ref_group){
+
+ FC.group = data.frame(matrix(ncol = 1, nrow = nrow(df_raw)))
+ colnames(FC.group) = Test_group
+ rownames(FC.group) = rownames(df_raw)
+
+ for (k in 1:nrow(df_raw)) {
+ signature = rownames(df_raw)[k]
+ test.table <- sample_info
+ test.table$scores <- df_raw[k,]
+ T2 <- test.table[test.table[, Group_column]==Test_group,] # "Group_test"; the selected column could be changed to your interested group comparison
+ T1 <- test.table[test.table[, Group_column]==Ref_group,] # "Group_test"; the selected column could be changed to your interested group comparison
+ FC.group[signature,] <- foldchange(mean(T2$scores),mean(T1$scores))
+ }
+ FCgroup <- data.frame(FC.group)
+ }
>
>
> library(ExperimentHub)
Loading required package: BiocGenerics
Loading required package: parallel
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 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.max, which.min
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
> library(SummarizedExperiment)
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
The following object is masked from 'package:ExperimentHub':
cache
The following object is masked from 'package:AnnotationHub':
cache
> dat = ExperimentHub()
snapshotDate(): 2021-05-18
> res = query(dat , "GSE13015")
> GSE13015 = res[["EH5429"]]
see ?GSE13015 and browseVignettes('GSE13015') for documentation
loading from cache
> data_matrix = assay(GSE13015)
> sample_ann = data.frame(colData(GSE13015))
>
>
> test_that("test fold_change", {
+ a = FCgroup = fold_change(df_raw = data_matrix[c(1:5),],
+ sample_info = sample_ann,
+ Group_column = "Group_test",
+ Test_group="Sepsis",
+ Ref_group="Control")
+ b = FCgroup = fold_change(df_raw = data_matrix[c(1:5),],
+ sample_info = sample_ann,
+ Group_column = "Group_test",
+ Test_group="Sepsis",
+ Ref_group="Control")
+
+ expect_that(a, equals(b))
+ })
Test passed
>
> proc.time()
user system elapsed
16.14 2.90 20.09
|
BloodGen3Module.Rcheck/tests_x64/test-fold_change.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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("gtools")
> library("testthat")
> library("BloodGen3Module")
Warning messages:
1: replacing previous import 'SummarizedExperiment::rowRanges' by 'matrixStats::rowRanges' when loading 'BloodGen3Module'
2: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'BloodGen3Module'
3: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'BloodGen3Module'
4: replacing previous import 'matrixStats::rowRanges' by 'SummarizedExperiment::rowRanges' when loading 'BloodGen3Module'
>
> fold_change = function(df_raw = df_raw,
+ sample_info = sample_info,
+ Group_column = Group_column,
+ Test_group=Test_group,
+ Ref_group=Ref_group){
+
+ FC.group = data.frame(matrix(ncol = 1, nrow = nrow(df_raw)))
+ colnames(FC.group) = Test_group
+ rownames(FC.group) = rownames(df_raw)
+
+ for (k in 1:nrow(df_raw)) {
+ signature = rownames(df_raw)[k]
+ test.table <- sample_info
+ test.table$scores <- df_raw[k,]
+ T2 <- test.table[test.table[, Group_column]==Test_group,] # "Group_test"; the selected column could be changed to your interested group comparison
+ T1 <- test.table[test.table[, Group_column]==Ref_group,] # "Group_test"; the selected column could be changed to your interested group comparison
+ FC.group[signature,] <- foldchange(mean(T2$scores),mean(T1$scores))
+ }
+ FCgroup <- data.frame(FC.group)
+ }
>
>
> library(ExperimentHub)
Loading required package: BiocGenerics
Loading required package: parallel
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 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.max, which.min
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
> library(SummarizedExperiment)
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
The following object is masked from 'package:ExperimentHub':
cache
The following object is masked from 'package:AnnotationHub':
cache
> dat = ExperimentHub()
snapshotDate(): 2021-05-18
> res = query(dat , "GSE13015")
> GSE13015 = res[["EH5429"]]
see ?GSE13015 and browseVignettes('GSE13015') for documentation
loading from cache
> data_matrix = assay(GSE13015)
> sample_ann = data.frame(colData(GSE13015))
>
>
> test_that("test fold_change", {
+ a = FCgroup = fold_change(df_raw = data_matrix[c(1:5),],
+ sample_info = sample_ann,
+ Group_column = "Group_test",
+ Test_group="Sepsis",
+ Ref_group="Control")
+ b = FCgroup = fold_change(df_raw = data_matrix[c(1:5),],
+ sample_info = sample_ann,
+ Group_column = "Group_test",
+ Test_group="Sepsis",
+ Ref_group="Control")
+
+ expect_that(a, equals(b))
+ })
Test passed
>
> proc.time()
user system elapsed
18.20 1.96 21.15
|
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BloodGen3Module.Rcheck/examples_i386/BloodGen3Module-Ex.timings
|
BloodGen3Module.Rcheck/examples_x64/BloodGen3Module-Ex.timings
|