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lgatto / synapter

Label-free data analysis pipeline for optimal identification and quantitation
https://lgatto.github.io/synapter/
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problems with master construction #113

Closed pavel-shliaha closed 8 years ago

pavel-shliaha commented 8 years ago

@sgibb I get the following message trying to construct master:

Generating unique proteotypic peptides... Error in duplicated(x) : object '.peptides' not found

the R script is in

Y:\RAW\pvs22_QTOF_DATA_data3\synapter2paper\kuharev2015\bugs_investigation\master_construction_bug

the R script references all the files necessary

pavel-shliaha commented 8 years ago

sorry now synapter fails to update

Warning: package 'BiocParallel' was built under R version 3.2.3 Warning in .recacheSubclasses(def@className, def, doSubclasses, env) : undefined subclass "externalRefMethod" of class "expressionORfunction"; definition not updated Warning in .recacheSubclasses(def@className, def, doSubclasses, env) : undefined subclass "externalRefMethod" of class "functionORNULL"; definition not updated ERROR: loading failed for 'i386'

sgibb commented 8 years ago

Are you sure you tried to install synapter 2.0 via devtools::install_github("lgatto/synapter@2.0", quick=TRUE)? Synapter 2.0 doesn't depend on BiocParallel anymore so this warning makes no sense to me. BTW would it be possible to update your R installation to R-3.2.4? 3.2.1 is quite old (> 9 month).

pavel-shliaha commented 8 years ago

sorry guys forgot to specify quick = TRUE