thomasp85 / msgfplus Goto Github PK

With the newest version of BiocManager (v3.15), MSGFplus has been removed. If possible, I would like to avoid installing the package from Github, because I do not want to install Rtools on every computer where I use the package.

Will there be an alternative way to install the package, either CRAN or BioConductor or a .tar.gz release?

Hi:
If I install the MSGFplus library using this line of code:

BiocManager::install("MSGFplus")

And, after that, if I try loading it, what I get is this warning message:

library(MSGFplus)
Error: package or namespace load failed for ‘MSGFplus’:
.onLoad failed in loadNamespace() for 'MSGFplus', details:
call: system2(.javaExecutable(), "-version", stderr = TRUE, stdout = TRUE)
error: 'CreateProcess' failed to run 'C:\PROGRA1\Java\JDK181.0_3 -version'

On the other hand, if I try installing this package after removing it using this code line:

devtools::install_github('thomasp85/MSGFplus')

This message appears:

* installing source package 'MSGFplus' ...
** using staged installation
** R
Error in .install_package_code_files(".", instdir) :
files in 'Collate' field missing from 'C:/Users/jvalf/AppData/Local/Temp/Rtmp6T1b6Q/R.INSTALL164c4e697167/MSGFplus/R':
msgfParGUI.R
ERROR: unable to collate and parse R files for package 'MSGFplus'
* removing 'C:/Users/jvalf/Documents/R/win-library/4.0/MSGFplus'

I just need it to work in order to install "proteomics" library. What do I need to do, exactly? Thanks in advance.

> library("rpx")
> px <- PXDataset("PXD000001")
> fas <- pxget(px, pxfiles(px)[8])
> mzf <- pxget(px, pxfiles(px)[6])
> library("MSGFplus")
> msgfpar <- msgfPar(database = fas,
+ instrument = 'HighRes',
+ tda = TRUE,
+ enzyme = 'Trypsin',
+ protocol = 'iTRAQ')
> idres <- runMSGF(msgfpar, mzf, memory=1000, import=FALSE)
java -Xmx1000M -jar "C:/Users/CCPguest/Documents/R/R-3.1.2/library/MSGFplus/MSGFPlus/MSGFPlus.jar" -s "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML" -o "C:/Users/CCPguest/Desktop/here/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzid" -d "erwinia_carotovora.fasta" -tda 1 -inst 1 -e 1 -protocol 2 

MS-GF+ Beta (v10072) (6/30/2014)
Loading database files...
Loading database finished (elapsed time: 0.74 sec)
Reading spectra...
javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,1]
Message: Content is not allowed in prolog.
    at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:601)
    at org.systemsbiology.jrap.stax.IndexParser.parseIndexes(IndexParser.java:176)
    at org.systemsbiology.jrap.stax.MSXMLParser.randomInits(MSXMLParser.java:117)
    at org.systemsbiology.jrap.stax.MSXMLParser.<init>(MSXMLParser.java:134)
    at edu.ucsd.msjava.parser.MzXMLSpectraMap.<init>(MzXMLSpectraMap.java:40)
    at edu.ucsd.msjava.msutil.SpectraAccessor.getSpecMap(SpectraAccessor.java:47)
    at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:259)
    at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:142)
    at edu.ucsd.msjava.ui.MSGFPlus.main(MSGFPlus.java:80)
javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,1]
Message: Content is not allowed in prolog.
    at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:601)
    at org.systemsbiology.jrap.stax.IndexParser.parseIndexes(IndexParser.java:176)
    at org.systemsbiology.jrap.stax.MSXMLParser.randomInits(MSXMLParser.java:117)
    at org.systemsbiology.jrap.stax.MSXMLParser.<init>(MSXMLParser.java:134)
    at edu.ucsd.msjava.parser.MzXMLSpectraMap.<init>(MzXMLSpectraMap.java:40)
    at edu.ucsd.msjava.parser.MzXMLSpectraIterator.<init>(MzXMLSpectraIterator.java:36)
    at edu.ucsd.msjava.parser.MzXMLSpectraIterator.<init>(MzXMLSpectraIterator.java:26)
    at edu.ucsd.msjava.msutil.SpectraAccessor.getSpecItr(SpectraAccessor.java:84)
    at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:259)
    at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:142)
    at edu.ucsd.msjava.ui.MSGFPlus.main(MSGFPlus.java:80)
Ignoring 0 profile spectra.
Ignoring 0 spectra having less than 10 peaks.
[Error] TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML includes no spectrum

The above code works on linux.

Annoyingly, runMSGF is apparently never run in any of the examples/vignette/tests in the package. Please fix this as I am under the impression that it might never have worked on Windows - make sure you test/run the main function of your package.

Title says it all. The question is whether R should just be run from the server in the first place?

Hi

I just want to report that there is a potential useful msgf+ option missing in msgfpar namely -addFeatures 0/1. This add extra variables calculated by msgf+ to each psm.
see msgf+ documentations :
https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355

greets

Hello,
I've tried to install MSGFplus both via Bioc and Github, without success. I encounter this issue:

`
Installing package into ‘/home/gian_ma/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)

• installing source package ‘MSGFplus’ ...
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded
  Warning in fun(libname, pkgname) : NAs introduced by coercion
  Error: package or namespace load failed for ‘MSGFplus’:
  .onLoad failed in loadNamespace() for 'MSGFplus', details:
  call: if (as.numeric(sub("."\d\.(\d).", "\1", javaVersion[1])) <
  error: missing value where TRUE/FALSE needed
  Error: loading failed
  Execution halted
  ERROR: loading failed
• removing ‘/home/gian_ma/R/x86_64-pc-linux-gnu-library/3.5/MSGFplus’
  Warning in install.packages :
  installation of package ‘./MSGFplus-master/’ had non-zero exit status
  `

My java version is:
$ java --version openjdk 10.0.1 2018-04-17 OpenJDK Runtime Environment (build 10.0.1+10-Ubuntu-3ubuntu1) OpenJDK 64-Bit Server VM (build 10.0.1+10-Ubuntu-3ubuntu1, mixed mode)
Ubuntu LTS 18.04

I've seen that someone experienced the same issue before, and it was supposed to be fixed.
I hope this is not trivial, and thank you for your help

It seems (quite surprisingly) that there is some confusion between the checkResFile/analysisSoftwareVersion functions and methods signatures:

* checking whether package ‘MSGFplus’ can be installed ... WARNING
Found the following significant warnings:
  Warning: For function ‘checkResFile’, signature ‘msgfRes’: argument in method definition changed from (object) to (file)
  Warning: For function ‘analysisSoftwareVersion’, signature ‘msgfRes’: argument in method definition changed from (object) to (file)

Easy to fix by change the function name or (I assume but not tested), renaming the function argument from file to object. Unless I'm missing anything here, happy to send another pull request.

I actually don't know whether there is any gain in this over creating a system() call, but it has to be investigated...

The version on Bioconductor uses dQuote the create the java path, which wrap the path in uni-code inverted quotes and fails in R. This has been confirmed on Linux and Windows.

The version on github works as expected (confirmed on linux). Could you commit the fix to Bioc, please.

Had a problem with the java version check in Oracle java.

1. Oracle java has versions such as 11.0.2 etc.
   The existing pattern match expects only a single digit in the major (11) part, and fails to load the Namespace completely.

Fixing the pattern match to allow more than one digit, allow loading of the Namespace with the warning about version.

Seems that the check should a) determine oracle vs open-jdk and have patterns that are appropriate to each.

How should the MSGFPlus.jar file be included? or should the user install it themselves? If so, how should we ensure version compatibility and set the correct path...

I have a Java version like:

> javaVersion
[1] "openjdk version \"11.0.7\" 2020-04-14"                                               
[2] "OpenJDK Runtime Environment (build 11.0.7+10-post-Debian-3deb10u1)"                  
[3] "OpenJDK 64-Bit Server VM (build 11.0.7+10-post-Debian-3deb10u1, mixed mode, sharing)"

It fails if install("MSGFplus") is used but I can install from GitHub. The package also fails on Bioconductor machine machv2 which runs macOS 10.14.6 Mojave for the same reason.

I have checked the document and can't find a way to include addFeatures=True to the R interface of MSGFplus to allow files to be post processed with Percolator. Is this something that can be included?
In that line, would it also be possible to allow the decoy abbreviation to be included/changed in this environment?

I currently have issues with runMSGF within a vignette on a windows server. The resulting mzid file is not where it is expected to be found. I spotted the following piece of run in the function that needs to be fixed

    if (Sys.info()["sysname"] == "Windows") {
        msgfPath <- paste0("\"", msgfPath, "\"")
    }

and use file.path() to construct the path to the file.

I can't yet guarantee that the above will fix my error, but this should nevertheless be fixed in devel and release.

Hi,

I get an error when I try to install MSGFplus on my linux machine. MS-GF+ standalone seems to work just fine.

My java version is:

    java -version
    openjdk version "1.8.0_25"
    OpenJDK Runtime Environment (build 1.8.0_25-b18)
    OpenJDK 64-Bit Server VM (build 25.25-b02, mixed mode)

The error is:

* installing *source* package ‘MSGFplus’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'MSGFplus', details:
  call: if (as.numeric(sub(".*\"\\d\\.(\\d).*", "\\1", javaVersion)) < 
  error: argument is of length zero
Error: loading failed
Execution halted
    ERROR: loading failed

Greetz

Hi @thomasp85 - I thought I had write access to the Bioc git repo, but apparently not:

$ MSGFplus git:(devel) git push upstream master 
FATAL: W any packages/MSGFplus l.gatto DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

Could you check, please.

Should it be up to the user, based on the description file, to have the correct version of Java installed on their system or should the package test for it on load+