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sneumann / mzR-playground

Playground area for the mzR package. The main code repository is now at https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR/
http://bioconductor.org/packages/devel/bioc/html/mzR.html
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header(mzdata) issue #8

Closed lgatto closed 13 years ago

lgatto commented 13 years ago

Data used: experiment 8150 from PRIDE Description: Fails: header(object) Works: header(object,i); header(object,i:j); header(object,1:length(object)) Note: experiment 12011 works fine, other files tested (mzData, mzML, mzXML) work fine.

library(mzR) Loading required package: Rcpp aa = openMSfile("PRIDE_Exp_mzData_Ac_8150.xml") 3: >PRIDE_Exp_mzData_Ac_8150.xml aa Read from disk. Mass Spectrometry file handle. Filename: PRIDE_Exp_mzData_Ac_8150.xml number scans: 212311 lowMZ: 0 highMZ: 0 startMZ: 0 endMZ: 0 dStartTime: 0 dEndTime: 0 hd = header(aa) Error in object@backend$getAllScanHeaderInfo() : error calling the data.frame function hd = header(aa,1:length(aa)) dim(hd) [1] 212311 20 nrow(hd)==length(aa) [1] TRUE

lgatto commented 13 years ago

Behaviour of header(aa) after header(aa,1:length(aa)) :

library(mzR) Loading required package: Rcpp aa = openMSfile("PRIDE_Exp_mzData_Ac_8150.xml") 3: >PRIDE_Exp_mzData_Ac_8150.xml hd = header(aa) Error in object@backend$getAllScanHeaderInfo() : error calling the data.frame function hd1 = header(aa,1:length(aa))

nrow(h1) == length(aa) Error in nrow(h1) : object 'h1' not found nrow(hd1) == length(aa) [1] TRUE hd2 = header(aa) * caught segfault * address 0xf26a3c0, cause 'memory not mapped' Segmentation fault

lgatto commented 13 years ago

declaredScansOnly default changed to fix this issue