Peter Hickey
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/DelayedMatrixStats |
| Branch: RELEASE_3_8 |
| Last Commit: eb5b390 |
| Last Changed Date: 2018-10-30 11:42:06 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:53:07 -0400 (Tue, 16 Apr 2019).
| Package 389/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DelayedMatrixStats 1.4.0 Peter Hickey
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DelayedMatrixStats |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DelayedMatrixStats.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DelayedMatrixStats_1.4.0.tar.gz |
| StartedAt: 2019-04-15 23:24:22 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:41:45 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 1042.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DelayedMatrixStats.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DelayedMatrixStats.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DelayedMatrixStats_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/DelayedMatrixStats.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 ‘DelayedMatrixStats/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DelayedMatrixStats’ version ‘1.4.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘DelayedMatrixStats’ 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 * 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 Missing objects imported by ':::' calls: ‘DelayedArray:::.execute_delayed_ops’ ‘DelayedArray:::get_Nindex_names_along’ Unexported objects imported by ':::' calls: ‘DelayedArray:::.get_ans_type’ ‘DelayedArray:::.reduce_array_dimensions’ ‘DelayedArray:::RleArraySeed’ ‘DelayedArray:::colblock_APPLY’ ‘DelayedArray:::get_Nindex_lengths’ ‘DelayedArray:::get_verbose_block_processing’ ‘DelayedArray:::set_dim’ ‘DelayedArray:::set_dimnames’ ‘DelayedArray:::subset_by_Nindex’ ‘DelayedArray:::to_linear_index’ See the note in ?`:::` about the use of this operator. * 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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 ‘/home/biocbuild/bbs-3.8-bioc/meat/DelayedMatrixStats.Rcheck/00check.log’ for details.
DelayedMatrixStats.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL DelayedMatrixStats ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘DelayedMatrixStats’ ... ** R ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘rowsum’ in package ‘DelayedMatrixStats’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (DelayedMatrixStats)
DelayedMatrixStats.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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.
> library(testthat)
> library(DelayedMatrixStats)
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: matrixStats
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply
Attaching package: 'DelayedMatrixStats'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyMissings, colAnyNAs, colAnys, colAvgsPerRowSet,
colCollapse, colCounts, colCummaxs, colCummins, colCumprods,
colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps,
colMadDiffs, colMads, colMeans2, colMedians, colOrderStats,
colProds, colQuantiles, colRanks, colSdDiffs, colSds, colSums2,
colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyMissings, rowAnyNAs, rowAnys,
rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins,
rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs,
rowLogSumExps, rowMadDiffs, rowMads, rowMeans2, rowMedians,
rowOrderStats, rowProds, rowQuantiles, rowRanks, rowSdDiffs,
rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
The following object is masked from 'package:base':
rowsum
>
> test_check("DelayedMatrixStats")
Loading required package: rhdf5
══ testthat results ═══════════════════════════════════════════════════════════
OK: 15140 SKIPPED: 0 FAILED: 0
> setAutoBlockSize(8)
automatic block size set to 8 bytes (was 1e+08)
> test_check("DelayedMatrixStats")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 15132 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
893.476 215.900 931.224
DelayedMatrixStats.Rcheck/DelayedMatrixStats-Ex.timings
| name | user | system | elapsed | |
| colAlls | 0.116 | 0.000 | 0.117 | |
| colAnyNAs | 0.196 | 0.004 | 0.199 | |
| colAvgsPerRowSet | 0.352 | 0.004 | 0.358 | |
| colCollapse | 0.172 | 0.004 | 0.179 | |
| colCounts | 0.144 | 0.004 | 0.150 | |
| colCummaxs | 0.224 | 0.000 | 0.234 | |
| colDiffs | 0.148 | 0.004 | 0.152 | |
| colIQRDiffs | 0.164 | 0.000 | 0.164 | |
| colIQRs | 0.008 | 0.000 | 0.007 | |
| colLogSumExps | 0.056 | 0.000 | 0.056 | |
| colMads | 0.148 | 0.000 | 0.149 | |
| colMeans2 | 0.020 | 0.000 | 0.022 | |
| colMedians | 0.024 | 0.000 | 0.023 | |
| colOrderStats | 0.048 | 0.000 | 0.047 | |
| colProds | 0.092 | 0.000 | 0.091 | |
| colQuantiles | 0.024 | 0.000 | 0.025 | |
| colRanks | 0.024 | 0.000 | 0.025 | |
| colSums2 | 0.02 | 0.00 | 0.02 | |
| colTabulates | 0.200 | 0.000 | 0.199 | |
| colVars | 0.076 | 0.000 | 0.077 | |
| colWeightedMads | 0.000 | 0.004 | 0.005 | |
| colWeightedMeans | 0.048 | 0.000 | 0.047 | |
| colWeightedMedians | 0.024 | 0.000 | 0.026 | |
| colWeightedVars | 0.108 | 0.000 | 0.107 | |
| colsum-HDF5Matrix-method | 0.320 | 0.176 | 0.515 | |
| colsum | 0.004 | 0.000 | 0.005 | |
| rowsum-DelayedMatrix-method | 0.032 | 0.008 | 0.038 | |