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CHECK report for Spectra on tokay1

This page was generated on 2021-05-06 12:33:44 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the Spectra package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1764/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Spectra 1.0.5  (landing page)
RforMassSpectrometry Package Maintainer
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/Spectra
Branch: RELEASE_3_12
Last Commit: b1c93af
Last Changed Date: 2020-11-25 10:18:47 -0400 (Wed, 25 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: Spectra
Version: 1.0.5
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Spectra.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Spectra_1.0.5.tar.gz
StartedAt: 2021-05-06 07:11:50 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 07:22:43 -0400 (Thu, 06 May 2021)
EllapsedTime: 653.3 seconds
RetCode: 0
Status:   OK   
CheckDir: Spectra.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Spectra.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Spectra_1.0.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/Spectra.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Spectra/DESCRIPTION' ... OK
* this is package 'Spectra' version '1.0.5'
* 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 'Spectra' 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 ... NOTE
Foreign function calls to a different package:
  .Call("_H5Dclose", ..., PACKAGE = "rhdf5")
  .Call("_H5Dopen", ..., PACKAGE = "rhdf5")
  .Call("_H5Dread", ..., PACKAGE = "rhdf5")
  .Call("_H5Fclose", ..., PACKAGE = "rhdf5")
  .Call("_H5Fopen", ..., PACKAGE = "rhdf5")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
Spectra 5.29   0.61   28.88
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
Spectra 5.94   0.33    25.5
* 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-3.12-bioc/meat/Spectra.Rcheck/00check.log'
for details.

Installation output

Spectra.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/Spectra_1.0.5.tar.gz && rm -rf Spectra.buildbin-libdir && mkdir Spectra.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Spectra.buildbin-libdir Spectra_1.0.5.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL Spectra_1.0.5.zip && rm Spectra_1.0.5.tar.gz Spectra_1.0.5.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  257k  100  257k    0     0  10.1M      0 --:--:-- --:--:-- --:--:-- 10.4M

install for i386

* installing *source* package 'Spectra' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'bin' in package 'Spectra'
** help
*** installing help indices
  converting help for package 'Spectra'
    finding HTML links ... done
    MsBackend                               html  
    finding level-2 HTML links ... done

    ProcessingStep                          html  
    Spectra                                 html  
    combinePeaks                            html  
    hidden_aliases                          html  
    joinPeaks                               html  
    spectra-plotting                        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 'Spectra' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Spectra' as Spectra_1.0.5.zip
* DONE (Spectra)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'Spectra' successfully unpacked and MD5 sums checked

Tests output

Spectra.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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("testthat")
> library("Spectra")
Loading required package: S4Vectors
Loading required package: stats4
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


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: BiocParallel
Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth

> 
> register(SerialParam())
> 
> sciex_file <- normalizePath(
+     dir(system.file("sciex", package = "msdata"), full.names = TRUE))
> cdf_file <- normalizePath(
+     dir(system.file("cdf", package = "msdata"), full.names = TRUE))
> 
> sciex_mzr <- backendInitialize(MsBackendMzR(), files = sciex_file)
> sciex_pks <- peaksData(sciex_mzr)
> fl <- normalizePath(
+     dir(system.file("proteomics", package = "msdata"), full.names = TRUE))
> tmt_mzr <- backendInitialize(MsBackendMzR(), files = fl[5])
> 
> sciex_hd5 <- backendInitialize(MsBackendHdf5Peaks(),
+                                data = spectraData(sciex_mzr),
+                                hdf5path = tempdir())
> 
> test_check("Spectra")
MsBackendDataFrame with 0 spectra
Error in .h5_read_bare(fid, "/header/modcount") : 
  HDF5. Dataset. Can't open object.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) : 
  HDF5. File accessibilty. Unable to open file.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) : 
  HDF5. File accessibilty. Unable to open file.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) : 
  HDF5. File accessibilty. Unable to open file.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) : 
  HDF5. File accessibilty. Unable to open file.
MsBackendHdf5Peaks with 3 spectra
    msLevel     rtime scanIndex
  <integer> <numeric> <integer>
1         1        NA         1
2         2        NA         1
3         2        NA         2
 ... 16 more variables/columns.

file(s):
 c
 d
MsBackendMzR with 0 spectra
MsBackendMzR with 1862 spectra
       msLevel     rtime scanIndex
     <integer> <numeric> <integer>
1            1     0.280         1
2            1     0.559         2
3            1     0.838         3
4            1     1.117         4
5            1     1.396         5
...        ...       ...       ...
1858         1   258.636       927
1859         1   258.915       928
1860         1   259.194       929
1861         1   259.473       930
1862         1   259.752       931
 ... 33 more variables/columns.

file(s):
20171016_POOL_POS_1_105-134.mzML
20171016_POOL_POS_3_105-134.mzML
MSn data (Spectra) with 0 spectra in a MsBackendDataFrame backend:
Lazy evaluation queue: 2 processing step(s)
MSn data (Spectra) with 1862 spectra in a MsBackendMzR backend:
       msLevel     rtime scanIndex
     <integer> <numeric> <integer>
1            1     0.280         1
2            1     0.559         2
3            1     0.838         3
4            1     1.117         4
5            1     1.396         5
...        ...       ...       ...
1858         1   258.636       927
1859         1   258.915       928
1860         1   259.194       929
1861         1   259.473       930
1862         1   259.752       931
 ... 33 more variables/columns.

file(s):
20171016_POOL_POS_1_105-134.mzML
20171016_POOL_POS_3_105-134.mzML
== Skipped tests ===============================================================
* Skipping on CRAN (15)
* empty test (2)

[ FAIL 0 | WARN 11 | SKIP 17 | PASS 1549 ]
> 
> proc.time()
   user  system elapsed 
 227.12   10.29  237.57

Spectra.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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("testthat")
> library("Spectra")
Loading required package: S4Vectors
Loading required package: stats4
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


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: BiocParallel
Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth

> 
> register(SerialParam())
> 
> sciex_file <- normalizePath(
+     dir(system.file("sciex", package = "msdata"), full.names = TRUE))
> cdf_file <- normalizePath(
+     dir(system.file("cdf", package = "msdata"), full.names = TRUE))
> 
> sciex_mzr <- backendInitialize(MsBackendMzR(), files = sciex_file)
> sciex_pks <- peaksData(sciex_mzr)
> fl <- normalizePath(
+     dir(system.file("proteomics", package = "msdata"), full.names = TRUE))
> tmt_mzr <- backendInitialize(MsBackendMzR(), files = fl[5])
> 
> sciex_hd5 <- backendInitialize(MsBackendHdf5Peaks(),
+                                data = spectraData(sciex_mzr),
+                                hdf5path = tempdir())
> 
> test_check("Spectra")
MsBackendDataFrame with 0 spectra
Error in .h5_read_bare(fid, "/header/modcount") : 
  HDF5. Dataset. Can't open object.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) : 
  HDF5. File accessibilty. Unable to open file.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) : 
  HDF5. File accessibilty. Unable to open file.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) : 
  HDF5. File accessibilty. Unable to open file.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) : 
  HDF5. File accessibilty. Unable to open file.
MsBackendHdf5Peaks with 3 spectra
    msLevel     rtime scanIndex
  <integer> <numeric> <integer>
1         1        NA         1
2         2        NA         1
3         2        NA         2
 ... 16 more variables/columns.

file(s):
 c
 d
MsBackendMzR with 0 spectra
MsBackendMzR with 1862 spectra
       msLevel     rtime scanIndex
     <integer> <numeric> <integer>
1            1     0.280         1
2            1     0.559         2
3            1     0.838         3
4            1     1.117         4
5            1     1.396         5
...        ...       ...       ...
1858         1   258.636       927
1859         1   258.915       928
1860         1   259.194       929
1861         1   259.473       930
1862         1   259.752       931
 ... 33 more variables/columns.

file(s):
20171016_POOL_POS_1_105-134.mzML
20171016_POOL_POS_3_105-134.mzML
MSn data (Spectra) with 0 spectra in a MsBackendDataFrame backend:
Lazy evaluation queue: 2 processing step(s)
MSn data (Spectra) with 1862 spectra in a MsBackendMzR backend:
       msLevel     rtime scanIndex
     <integer> <numeric> <integer>
1            1     0.280         1
2            1     0.559         2
3            1     0.838         3
4            1     1.117         4
5            1     1.396         5
...        ...       ...       ...
1858         1   258.636       927
1859         1   258.915       928
1860         1   259.194       929
1861         1   259.473       930
1862         1   259.752       931
 ... 33 more variables/columns.

file(s):
20171016_POOL_POS_1_105-134.mzML
20171016_POOL_POS_3_105-134.mzML
== Skipped tests ===============================================================
* Skipping on CRAN (15)
* empty test (2)

[ FAIL 0 | WARN 11 | SKIP 17 | PASS 1549 ]
> 
> proc.time()
   user  system elapsed 
 252.18    5.84  257.57

Example timings

Spectra.Rcheck/examples_i386/Spectra-Ex.timings

nameusersystemelapsed
MsBackend0.250.000.25
ProcessingStep000
Spectra 5.29 0.6128.88
combinePeaks0.030.000.03
joinPeaks000
spectra-plotting0.330.000.33

Spectra.Rcheck/examples_x64/Spectra-Ex.timings

nameusersystemelapsed
MsBackend0.300.000.29
ProcessingStep000
Spectra 5.94 0.3325.50
combinePeaks0.030.000.03
joinPeaks0.010.000.01
spectra-plotting0.330.000.33