Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:07:00 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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

CHECK results for projectR on palomino4


To the developers/maintainers of the projectR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/projectR.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.

raw results

Package 1488/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
projectR 1.13.0  (landing page)
Genevieve Stein-O'Brien
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/projectR
git_branch: master
git_last_commit: 8f9dc56
git_last_commit_date: 2022-04-26 11:54:02 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    ERROR  skippedskipped

Summary

Package: projectR
Version: 1.13.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:projectR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings projectR_1.13.0.tar.gz
StartedAt: 2022-06-24 04:36:38 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:40:29 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 230.8 seconds
RetCode: 0
Status:   OK  
CheckDir: projectR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:projectR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings projectR_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/projectR.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'projectR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'projectR' version '1.13.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'projectR' 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 ... 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
* 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
alluvialMat: no visible binding for global variable 'celltype'
alluvialMat: no visible binding for global variable 'variable'
alluvialMat: no visible binding for global variable 'value'
alluvialMat: no visible binding for global variable 'nCells'
alluvialMat: no visible binding for global variable 'nCells_per_type'
alluvialMat: no visible binding for global variable
  'nCells_per_pattern'
alluvialMat: no visible binding for global variable 'prop'
Undefined global functions or variables:
  celltype nCells nCells_per_pattern nCells_per_type prop value
  variable
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
projectR-methods 28.86   0.03   28.92
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/projectR.Rcheck/00check.log'
for details.



Installation output

projectR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/projectR_1.13.0.tar.gz && rm -rf projectR.buildbin-libdir && mkdir projectR.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=projectR.buildbin-libdir projectR_1.13.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL projectR_1.13.0.zip && rm projectR_1.13.0.tar.gz projectR_1.13.0.zip
###
##############################################################################
##############################################################################


  % 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  868k  100  868k    0     0  7282k      0 --:--:-- --:--:-- --:--:-- 7358k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'projectR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
* MD5 sums
packaged installation of 'projectR' as projectR_1.13.0.zip
* DONE (projectR)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'projectR' successfully unpacked and MD5 sums checked

Tests output

projectR.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
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(projectR)
> 
> test_check("projectR")

This is CoGAPS version 3.17.0 
Running Standard CoGAPS on p.RNAseq6l3c3t (108 genes and 54 samples) with parameters:

-- Standard Parameters --
nPatterns            5 
nIterations          50000 
seed                 460 
sparseOptimization   FALSE 

-- Sparsity Parameters --
alpha          0.01 
maxGibbsMass   100 

Data Model: Dense, Normal
Sampler Type: Sequential
Loading Data...Done! (00:00:00)
-- Equilibration Phase --
1000 of 50000, Atoms: 193(A), 121(P), ChiSq: 53513, Time: 00:00:00 / 00:00:00
2000 of 50000, Atoms: 261(A), 135(P), ChiSq: 37765, Time: 00:00:00 / 00:00:00
3000 of 50000, Atoms: 271(A), 160(P), ChiSq: 35440, Time: 00:00:00 / 00:00:00
4000 of 50000, Atoms: 274(A), 168(P), ChiSq: 34206, Time: 00:00:00 / 00:00:00
5000 of 50000, Atoms: 307(A), 166(P), ChiSq: 33348, Time: 00:00:00 / 00:00:00
6000 of 50000, Atoms: 327(A), 185(P), ChiSq: 32401, Time: 00:00:01 / 00:00:22
7000 of 50000, Atoms: 323(A), 188(P), ChiSq: 32096, Time: 00:00:01 / 00:00:19
8000 of 50000, Atoms: 335(A), 186(P), ChiSq: 31736, Time: 00:00:01 / 00:00:16
9000 of 50000, Atoms: 341(A), 200(P), ChiSq: 31550, Time: 00:00:01 / 00:00:14
10000 of 50000, Atoms: 370(A), 193(P), ChiSq: 30599, Time: 00:00:02 / 00:00:25
11000 of 50000, Atoms: 385(A), 201(P), ChiSq: 30372, Time: 00:00:02 / 00:00:23
12000 of 50000, Atoms: 380(A), 206(P), ChiSq: 30521, Time: 00:00:02 / 00:00:20
13000 of 50000, Atoms: 388(A), 207(P), ChiSq: 30361, Time: 00:00:02 / 00:00:19
14000 of 50000, Atoms: 413(A), 197(P), ChiSq: 30094, Time: 00:00:03 / 00:00:26
15000 of 50000, Atoms: 409(A), 212(P), ChiSq: 30182, Time: 00:00:03 / 00:00:24
16000 of 50000, Atoms: 402(A), 215(P), ChiSq: 29858, Time: 00:00:03 / 00:00:22
17000 of 50000, Atoms: 407(A), 207(P), ChiSq: 30041, Time: 00:00:03 / 00:00:21
18000 of 50000, Atoms: 408(A), 230(P), ChiSq: 29859, Time: 00:00:04 / 00:00:26
19000 of 50000, Atoms: 406(A), 211(P), ChiSq: 29878, Time: 00:00:04 / 00:00:25
20000 of 50000, Atoms: 410(A), 224(P), ChiSq: 29746, Time: 00:00:04 / 00:00:23
21000 of 50000, Atoms: 429(A), 233(P), ChiSq: 29572, Time: 00:00:05 / 00:00:27
22000 of 50000, Atoms: 459(A), 227(P), ChiSq: 29168, Time: 00:00:05 / 00:00:26
23000 of 50000, Atoms: 486(A), 229(P), ChiSq: 29018, Time: 00:00:05 / 00:00:25
24000 of 50000, Atoms: 495(A), 228(P), ChiSq: 28564, Time: 00:00:05 / 00:00:24
25000 of 50000, Atoms: 481(A), 222(P), ChiSq: 28206, Time: 00:00:06 / 00:00:27
26000 of 50000, Atoms: 460(A), 232(P), ChiSq: 28167, Time: 00:00:06 / 00:00:26
27000 of 50000, Atoms: 465(A), 264(P), ChiSq: 28291, Time: 00:00:06 / 00:00:25
28000 of 50000, Atoms: 476(A), 238(P), ChiSq: 28157, Time: 00:00:07 / 00:00:28
29000 of 50000, Atoms: 462(A), 243(P), ChiSq: 28311, Time: 00:00:07 / 00:00:27
30000 of 50000, Atoms: 473(A), 228(P), ChiSq: 28189, Time: 00:00:07 / 00:00:26
31000 of 50000, Atoms: 473(A), 237(P), ChiSq: 28212, Time: 00:00:08 / 00:00:29
32000 of 50000, Atoms: 474(A), 238(P), ChiSq: 28215, Time: 00:00:08 / 00:00:28
33000 of 50000, Atoms: 486(A), 248(P), ChiSq: 28219, Time: 00:00:08 / 00:00:27
34000 of 50000, Atoms: 466(A), 251(P), ChiSq: 28211, Time: 00:00:08 / 00:00:26
35000 of 50000, Atoms: 473(A), 237(P), ChiSq: 28263, Time: 00:00:09 / 00:00:28
36000 of 50000, Atoms: 480(A), 246(P), ChiSq: 28248, Time: 00:00:09 / 00:00:27
37000 of 50000, Atoms: 480(A), 240(P), ChiSq: 28187, Time: 00:00:09 / 00:00:26
38000 of 50000, Atoms: 484(A), 236(P), ChiSq: 28175, Time: 00:00:10 / 00:00:28
39000 of 50000, Atoms: 495(A), 233(P), ChiSq: 28217, Time: 00:00:10 / 00:00:28
40000 of 50000, Atoms: 478(A), 241(P), ChiSq: 28221, Time: 00:00:10 / 00:00:27
41000 of 50000, Atoms: 467(A), 230(P), ChiSq: 28289, Time: 00:00:11 / 00:00:29
42000 of 50000, Atoms: 463(A), 230(P), ChiSq: 28203, Time: 00:00:11 / 00:00:28
43000 of 50000, Atoms: 474(A), 237(P), ChiSq: 28153, Time: 00:00:11 / 00:00:27
44000 of 50000, Atoms: 477(A), 243(P), ChiSq: 28274, Time: 00:00:11 / 00:00:27
45000 of 50000, Atoms: 469(A), 227(P), ChiSq: 28260, Time: 00:00:12 / 00:00:28
46000 of 50000, Atoms: 488(A), 239(P), ChiSq: 28129, Time: 00:00:12 / 00:00:28
47000 of 50000, Atoms: 486(A), 238(P), ChiSq: 28175, Time: 00:00:12 / 00:00:27
48000 of 50000, Atoms: 472(A), 237(P), ChiSq: 28198, Time: 00:00:13 / 00:00:29
49000 of 50000, Atoms: 465(A), 231(P), ChiSq: 28162, Time: 00:00:13 / 00:00:28
50000 of 50000, Atoms: 474(A), 230(P), ChiSq: 28154, Time: 00:00:13 / 00:00:27
-- Sampling Phase --
1000 of 50000, Atoms: 468(A), 252(P), ChiSq: 28178, Time: 00:00:13 / 00:00:27
2000 of 50000, Atoms: 468(A), 241(P), ChiSq: 28192, Time: 00:00:14 / 00:00:28
3000 of 50000, Atoms: 480(A), 248(P), ChiSq: 28200, Time: 00:00:14 / 00:00:28
4000 of 50000, Atoms: 474(A), 239(P), ChiSq: 28234, Time: 00:00:14 / 00:00:27
5000 of 50000, Atoms: 462(A), 244(P), ChiSq: 28171, Time: 00:00:15 / 00:00:28
6000 of 50000, Atoms: 488(A), 236(P), ChiSq: 28167, Time: 00:00:15 / 00:00:28
7000 of 50000, Atoms: 464(A), 237(P), ChiSq: 28211, Time: 00:00:15 / 00:00:27
8000 of 50000, Atoms: 465(A), 237(P), ChiSq: 28206, Time: 00:00:15 / 00:00:27
9000 of 50000, Atoms: 479(A), 244(P), ChiSq: 28197, Time: 00:00:16 / 00:00:28
10000 of 50000, Atoms: 465(A), 227(P), ChiSq: 28176, Time: 00:00:16 / 00:00:28
11000 of 50000, Atoms: 449(A), 256(P), ChiSq: 28205, Time: 00:00:16 / 00:00:27
12000 of 50000, Atoms: 470(A), 239(P), ChiSq: 28234, Time: 00:00:17 / 00:00:28
13000 of 50000, Atoms: 480(A), 229(P), ChiSq: 28206, Time: 00:00:17 / 00:00:28
14000 of 50000, Atoms: 462(A), 235(P), ChiSq: 28212, Time: 00:00:17 / 00:00:27
15000 of 50000, Atoms: 464(A), 253(P), ChiSq: 28298, Time: 00:00:17 / 00:00:27
16000 of 50000, Atoms: 457(A), 244(P), ChiSq: 28206, Time: 00:00:18 / 00:00:28
17000 of 50000, Atoms: 463(A), 237(P), ChiSq: 28262, Time: 00:00:18 / 00:00:27
18000 of 50000, Atoms: 483(A), 233(P), ChiSq: 28215, Time: 00:00:18 / 00:00:27
19000 of 50000, Atoms: 485(A), 236(P), ChiSq: 28193, Time: 00:00:19 / 00:00:28
20000 of 50000, Atoms: 480(A), 235(P), ChiSq: 28196, Time: 00:00:19 / 00:00:28
21000 of 50000, Atoms: 484(A), 231(P), ChiSq: 28195, Time: 00:00:19 / 00:00:27
22000 of 50000, Atoms: 464(A), 244(P), ChiSq: 28188, Time: 00:00:20 / 00:00:28
23000 of 50000, Atoms: 461(A), 232(P), ChiSq: 28176, Time: 00:00:20 / 00:00:28
24000 of 50000, Atoms: 466(A), 237(P), ChiSq: 28293, Time: 00:00:20 / 00:00:27
25000 of 50000, Atoms: 482(A), 242(P), ChiSq: 28177, Time: 00:00:20 / 00:00:27
26000 of 50000, Atoms: 456(A), 234(P), ChiSq: 28210, Time: 00:00:21 / 00:00:28
27000 of 50000, Atoms: 464(A), 247(P), ChiSq: 28189, Time: 00:00:21 / 00:00:27
28000 of 50000, Atoms: 472(A), 246(P), ChiSq: 28211, Time: 00:00:21 / 00:00:27
29000 of 50000, Atoms: 496(A), 236(P), ChiSq: 28206, Time: 00:00:22 / 00:00:28
30000 of 50000, Atoms: 443(A), 233(P), ChiSq: 28246, Time: 00:00:22 / 00:00:28
31000 of 50000, Atoms: 476(A), 240(P), ChiSq: 28239, Time: 00:00:22 / 00:00:27
32000 of 50000, Atoms: 479(A), 236(P), ChiSq: 28141, Time: 00:00:22 / 00:00:27
33000 of 50000, Atoms: 463(A), 243(P), ChiSq: 28218, Time: 00:00:23 / 00:00:28
34000 of 50000, Atoms: 473(A), 227(P), ChiSq: 28252, Time: 00:00:23 / 00:00:27
35000 of 50000, Atoms: 474(A), 228(P), ChiSq: 28206, Time: 00:00:23 / 00:00:27
36000 of 50000, Atoms: 463(A), 240(P), ChiSq: 28208, Time: 00:00:24 / 00:00:28
37000 of 50000, Atoms: 476(A), 231(P), ChiSq: 28178, Time: 00:00:24 / 00:00:27
38000 of 50000, Atoms: 478(A), 235(P), ChiSq: 28179, Time: 00:00:24 / 00:00:27
39000 of 50000, Atoms: 473(A), 223(P), ChiSq: 28236, Time: 00:00:25 / 00:00:28
40000 of 50000, Atoms: 469(A), 220(P), ChiSq: 28184, Time: 00:00:25 / 00:00:28
41000 of 50000, Atoms: 481(A), 234(P), ChiSq: 28158, Time: 00:00:25 / 00:00:27
42000 of 50000, Atoms: 463(A), 223(P), ChiSq: 28178, Time: 00:00:26 / 00:00:28
43000 of 50000, Atoms: 478(A), 244(P), ChiSq: 28254, Time: 00:00:26 / 00:00:28
44000 of 50000, Atoms: 474(A), 243(P), ChiSq: 28261, Time: 00:00:26 / 00:00:27
45000 of 50000, Atoms: 477(A), 232(P), ChiSq: 28195, Time: 00:00:26 / 00:00:27
46000 of 50000, Atoms: 468(A), 231(P), ChiSq: 28165, Time: 00:00:27 / 00:00:28
47000 of 50000, Atoms: 453(A), 237(P), ChiSq: 28200, Time: 00:00:27 / 00:00:27
48000 of 50000, Atoms: 478(A), 228(P), ChiSq: 28184, Time: 00:00:27 / 00:00:27
49000 of 50000, Atoms: 472(A), 240(P), ChiSq: 28202, Time: 00:00:28 / 00:00:28
50000 of 50000, Atoms: 495(A), 238(P), ChiSq: 28210, Time: 00:00:28 / 00:00:28
[1] "93 row names matched between data and loadings"
[1] "Updated dimension of data: 93 9"
[1] "93 row names matched between data and loadings"
[1] "Updated dimension of data: 93 9"
[1] "93 row names matched between data and loadings"
[1] "Updated dimension of data: 93 9"
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 24 ]

[ FAIL 0 | WARN 13 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  36.62    0.60   37.18 

Example timings

projectR.Rcheck/projectR-Ex.timings

nameusersystemelapsed
alluvialMat0.50.00.5
aucMat0.080.000.08
cluster2pattern-methods0.700.020.72
clusterPlotR-methods000
correlateR0.100.000.09
geneMatchR0.010.010.03
intersectoR-methods0.000.010.01
projectR-methods28.86 0.0328.92
rotatoR000