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This page was generated on 2022-06-24 11:07:16 -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 Spectra on palomino4


To the developers/maintainers of the Spectra package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Spectra.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 1879/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Spectra 1.7.0  (landing page)
RforMassSpectrometry Package Maintainer
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/Spectra
git_branch: master
git_last_commit: 19c4dd4
git_last_commit_date: 2022-04-26 12:08:00 -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    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Spectra
Version: 1.7.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Spectra.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings Spectra_1.7.0.tar.gz
StartedAt: 2022-06-24 06:04:58 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 06:13:11 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 492.9 seconds
RetCode: 0
Status:   OK  
CheckDir: Spectra.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Spectra.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings Spectra_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/Spectra.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 'Spectra/DESCRIPTION' ... OK
* this is package 'Spectra' version '1.7.0'
* 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
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
Spectra     10.97   0.60  117.21
plotMzDelta  2.59   0.19   19.59
neutralLoss  1.18   0.09   16.97
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/Spectra.Rcheck/00check.log'
for details.



Installation output

Spectra.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/Spectra_1.7.0.tar.gz && rm -rf Spectra.buildbin-libdir && mkdir Spectra.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Spectra.buildbin-libdir Spectra_1.7.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL Spectra_1.7.0.zip && rm Spectra_1.7.0.tar.gz Spectra_1.7.0.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  665k  100  665k    0     0  6159k      0 --:--:-- --:--:-- --:--:-- 6222k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'Spectra' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 'Spectra' as Spectra_1.7.0.zip
* DONE (Spectra)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'Spectra' successfully unpacked and MD5 sums checked

Tests output

Spectra.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("Spectra")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: BiocParallel
Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth


Attaching package: 'Spectra'

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

    addProcessing

> 
> 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")
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 accessibility. Unable to open file.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) : 
  HDF5. File accessibility. Unable to open file.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) : 
  HDF5. File accessibility. Unable to open file.
Error in try(.Call("_H5Fopen", x, 0L, fapl@ID, PACKAGE = "rhdf5")) : 
  HDF5. File accessibility. 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)
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
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
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
NULL
[ FAIL 0 | WARN 10 | SKIP 7 | PASS 1817 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (6)
• empty test (1)

[ FAIL 0 | WARN 10 | SKIP 7 | PASS 1817 ]
Deleting unused snapshots:
• plotting-functions/plot-single-spectrum-labels-ass.svg
• plotting-functions/plot-single-spectrum-labels.svg
• plotting-functions/plot-single-spectrum-xlim.svg
• plotting-functions/plotspectra-asp05.svg
• plotting-functions/plotspectra-asp2.svg
• plotting-functions/plotspectra-color-peaks-label-labelcol.svg
• plotting-functions/plotspectra-color-peaks-label.svg
• plotting-functions/plotspectra-color-peaks.svg
• plotting-functions/plotspectramirror-match-color-labelcol.svg
• plotting-functions/plotspectramirror-match-color.svg
• plotting-functions/plotspectramirror-same.svg
• plotting-functions/plotspectraoverlay-no-axes.svg
• plotting-functions/plotspectraoverlay-xlim.svg
> 
> proc.time()
   user  system elapsed 
 210.15    9.60  242.11 

Example timings

Spectra.Rcheck/Spectra-Ex.timings

nameusersystemelapsed
MsBackend0.250.000.25
Spectra 10.97 0.60117.21
combinePeaks0.050.000.04
countIdentifications0.390.014.05
filterFourierTransformArtefacts0.290.034.16
joinPeaks000
neutralLoss 1.18 0.0916.97
plotMzDelta 2.59 0.1919.59
spectra-plotting0.410.000.41