Multiple platform build/check report for BioC 3.14 - CHECK results for recountmethylation on tokay2

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*

Package: recountmethylation

Version: 1.4.5

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:recountmethylation.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings recountmethylation_1.4.5.tar.gz

StartedAt: 2022-04-13 01:23:28 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 01:26:19 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 171.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: recountmethylation.Rcheck

Warnings: 2

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:recountmethylation.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings recountmethylation_1.4.5.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/recountmethylation.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 'recountmethylation/DESCRIPTION' ... OK
* this is package 'recountmethylation' version '1.4.5'
* 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 'recountmethylation' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
* 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 ... WARNING
'::' or ':::' imports not declared from:
  'DelayedMatrixStats' 'basilisk' 'reticulate'
Namespace in Imports field not imported from: 'IlluminaHumanMethylation450kmanifest'
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'ba.background' 'ba.biotinstaining.grn' 'ba.biotinstaining.red'
  'ba.bisulfiteconv1.grn' 'ba.bisulfiteconv1.red' 'ba.bisulfiteconv2'
  'ba.extension.grn' 'ba.extension.red' 'ba.hybridization.hi.vs.med'
  'ba.hybridization.med.vs.low' 'ba.nonpolymorphic.grn'
  'ba.nonpolymorphic.red' 'ba.restoration' 'ba.specificity1.grn'
  'ba.specificity1.red' 'ba.specificity2' 'ba.targetremoval1'
  'ba.targetremoval2' 'setup_sienv'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get_fh : <anonymous>: no visible global function definition for
  'make_fhmatrix_autolabel'
make_si : <anonymous>: no visible global function definition for
  'make_hnsw_si'
query_si: no visible binding for global variable 'v'
query_si : <anonymous>: no visible global function definition for
  'make_dfk_sampleid'
Undefined global functions or variables:
  make_dfk_sampleid make_fhmatrix_autolabel make_hnsw_si v
* checking Rd files ... NOTE
prepare_Rd: query_si.Rd:33-35: Dropping empty section \value
* 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 ... WARNING
'library' or 'require' call not declared from: 'minfiData'
* 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
bactrl        11.81   1.31   13.22
gds_idat2rg    7.21   0.61   19.69
gds_idatquery  1.20   0.26   15.81
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
bactrl        13.54   0.59   14.16
gds_idat2rg    7.48   0.58   24.08
gds_idatquery  1.88   0.30   13.67
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-servermatrix.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-servermatrix.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: 2 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/recountmethylation.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/recountmethylation_1.4.5.tar.gz && rm -rf recountmethylation.buildbin-libdir && mkdir recountmethylation.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=recountmethylation.buildbin-libdir recountmethylation_1.4.5.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL recountmethylation_1.4.5.zip && rm recountmethylation_1.4.5.tar.gz recountmethylation_1.4.5.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
  8 4111k    8  339k    0     0   535k      0  0:00:07 --:--:--  0:00:07  535k
 39 4111k   39 1620k    0     0   991k      0  0:00:04  0:00:01  0:00:03  990k
 90 4111k   90 3707k    0     0  1409k      0  0:00:02  0:00:02 --:--:-- 1409k
100 4111k  100 4111k    0     0  1479k      0  0:00:02  0:00:02 --:--:-- 1479k

install for i386

* installing *source* package 'recountmethylation' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'recountmethylation'
    finding HTML links ... done
    ba                                      html  
    bactrl                                  html  
    bathresh                                html  
    data_mdpost                             html  
    gds_idat2rg                             html  
    gds_idatquery                           html  
    get_crossreactive_cpgs                  html  
    get_fh                                  html  
    get_qcsignal                            html  
    get_rmdl                                html  
    get_servermatrix                        html  
    getdb                                   html  
    getrg                                   html  
    hread                                   html  
    make_si                                 html  
    matchds_1to2                            html  
    query_si                                html  
    rgse                                    html  
    servermatrix                            html  
    setup_sienv                             html  
    smfilt                                  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 'recountmethylation' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'recountmethylation' as recountmethylation_1.4.5.zip
* DONE (recountmethylation)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'recountmethylation' successfully unpacked and MD5 sums checked


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.

> testthat::context("Test the server matrix properties")
> 
> testthat::test_that("Properties of server matrix returned from get_rmdl 
+     and servermatrix", {
+     sm <- recountmethylation::get_servermatrix()
+     testthat::expect_true(is(sm, "matrix"))
+     testthat::expect_equal(ncol(sm), 4)
+     testthat::expect_true(is(sm[,1], "character"))
+ })
Test passed 
> 
> proc.time()
   user  system elapsed 
   1.60    0.15    2.03


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.

> testthat::context("Test the server matrix properties")
> 
> testthat::test_that("Properties of server matrix returned from get_rmdl 
+     and servermatrix", {
+     sm <- recountmethylation::get_servermatrix()
+     testthat::expect_true(is(sm, "matrix"))
+     testthat::expect_equal(ncol(sm), 4)
+     testthat::expect_true(is(sm[,1], "character"))
+ })
Test passed 
> 
> proc.time()
   user  system elapsed 
   1.53    0.26    1.98

name	user	system	elapsed
bactrl	11.81	1.31	13.22
bathresh	0	0	0
data_mdpost	0.00	0.00	0.03
gds_idat2rg	7.21	0.61	19.69
gds_idatquery	1.20	0.26	15.81
get_crossreactive_cpgs	0.34	0.05	0.87
get_fh	0	0	0
get_qcsignal	2.97	0.22	3.19
get_rmdl	0.62	0.41	1.32
get_servermatrix	0	0	0
getdb	0	0	0
getrg	0.24	0.11	0.38
hread	0.01	0.00	0.02
make_si	0	0	0
matchds_1to2	0	0	0
query_si	0	0	0
rgse	0.21	0.10	0.31
servermatrix	0.04	0.00	0.25
smfilt	0	0	0

name	user	system	elapsed
bactrl	13.54	0.59	14.16
bathresh	0	0	0
data_mdpost	0.02	0.00	0.01
gds_idat2rg	7.48	0.58	24.08
gds_idatquery	1.88	0.30	13.67
get_crossreactive_cpgs	0.14	0.01	0.16
get_fh	0	0	0
get_qcsignal	2.48	0.08	2.56
get_rmdl	0.53	0.08	0.81
get_servermatrix	0	0	0
getdb	0	0	0
getrg	0.34	0.03	0.37
hread	0.02	0.00	0.02
make_si	0	0	0
matchds_1to2	0	0	0
query_si	0	0	0
rgse	0.15	0.01	0.17
servermatrix	0.02	0.00	0.22
smfilt	0.01	0.00	0.02

CHECK results for recountmethylation on tokay2

Summary

Command output

Installation output

Tests output

Example timings