Sorry for the additional email. It turns out there is additional information in the file /Users/biocbuild/bbs-3.3-bioc/meat/SWATH2stats.Rcheck/tests/test-all.Rout.fail on morelia (and similar on zin2). Below are the contents of each.
From morelia
R Under development (unstable) (2015-11-08 r69614) -- "Unsuffered Consequences" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin13.4.0 (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)
test_check("SWATH2stats")
Loading required package: SWATH2stats
1. Error: data conversion ------------------------------------------------------
The number of transitions annotated and measured do not match in the
following transitions:
1069078_FIIDPAAVITGR_2, 1069082_FIIDPAAVITGR_2,
1069080_FIIDPAAVITGR_2, 1069071_FIIDPAAVITGR_2,
1069078_FIIDPAAVITGR_2, 1069082_FIIDPAAVITGR_2,
1069080_FIIDPAAVITGR_2, 1069071_FIIDPAAVITGR_2,
1069084_FIIDPAAVITGR_2, 1069076_FIIDPAAVITGR_2
1: withCallingHandlers(eval(code, new_test_environment), error =
capture_calls, message = function(c) invokeRestart("muffleMessage"))
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: expect_that(disaggregate(data.max.test2), shows_message("The
library contains between 4 and 6 transitions per precursor.",
fixed = TRUE)) at test_convert.R:50
5: condition(object)
6: evaluate_promise(expr)
7: with_sink(temp, withCallingHandlers(withVisible(code), warning =
wHandler, message = mHandler))
8: withCallingHandlers(withVisible(code), warning = wHandler, message
= mHandler)
9: withVisible(code)
10: disaggregate(data.max.test2)
11: stop(paste("The number of transitions annotated and measured do
not match in the following transitions:\n",
paste(unlist(n.transitions[n.transitions2 != n.transitions4]),
collapse = ", ")))
testthat results
================================================================
OK: 46 SKIPPED: 0 FAILED: 1
1. Error: data conversion
Error: testthat unit tests failed
Execution halted
From zin2
R Under development (unstable) (2015-11-08 r69614) -- "Unsuffered Consequences" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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)
test_check("SWATH2stats")
Loading required package: SWATH2stats
1. Error: data conversion ------------------------------------------------------
The number of transitions annotated and measured do not match in the
following transitions:
1069078_FIIDPAAVITGR_2, 1069082_FIIDPAAVITGR_2,
1069080_FIIDPAAVITGR_2, 1069071_FIIDPAAVITGR_2,
1069078_FIIDPAAVITGR_2, 1069082_FIIDPAAVITGR_2,
1069080_FIIDPAAVITGR_2, 1069071_FIIDPAAVITGR_2,
1069084_FIIDPAAVITGR_2, 1069076_FIIDPAAVITGR_2
1: withCallingHandlers(eval(code, new_test_environment), error =
capture_calls, message = function(c) invokeRestart("muffleMessage"))
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: expect_that(disaggregate(data.max.test2), shows_message("The
library contains between 4 and 6 transitions per precursor.",
fixed = TRUE)) at test_convert.R:50
5: condition(object)
6: evaluate_promise(expr)
7: with_sink(temp, withCallingHandlers(withVisible(code), warning =
wHandler, message = mHandler))
8: withCallingHandlers(withVisible(code), warning = wHandler, message
= mHandler)
9: withVisible(code)
10: disaggregate(data.max.test2)
11: stop(paste("The number of transitions annotated and measured do
not match in the following transitions:\n",
paste(unlist(n.transitions[n.transitions2 != n.transitions4]),
collapse = ", ")))
testthat results
================================================================
OK: 46 SKIPPED: 0 FAILED: 1
1. Error: data conversion
Error: testthat unit tests failed
Execution halted
Hope this helps,
Brian
?
On Wed, Nov 11, 2015 at 12:29 PM, Brian Long <brian at bioconductor.org> wrote:
Hi Peter, Jim is right, the content of /Users/biocbuild/bbs-3.3-bioc/meat/SWATH2stats.Rcheck/00check.log is nearly identical to what you see on the web <http://bioconductor.org/checkResults/devel/bioc-LATEST/SWATH2stats/morelia-checksrc.html>. The only difference, is that the copy on web is a day older (since the build report for today hasn?t been generated yet). Here?s content of /Users/biocbuild/bbs-3.3-bioc/meat/SWATH2stats.Rcheck/00check.log from the morelia build server : * using log directory ?/Users/biocbuild/bbs-3.3-bioc/meat/SWATH2stats.Rcheck? * using R Under development (unstable) (2015-11-08 r69614) * using platform: x86_64-apple-darwin13.4.0 (64-bit) * using session charset: UTF-8 * using option ?--no-vignettes? * checking for file ?SWATH2stats/DESCRIPTION? ... OK * checking extension type ... Package * this is package ?SWATH2stats? version ?1.1.2? * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: ?imsbInfer? * 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 for sufficient/correct file permissions ... OK * checking whether package ?SWATH2stats? can be installed ... [2s/2s] 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 loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * 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 sizes of PDF files under ?inst/doc? ... OK * checking installed files from ?inst/doc? ... OK * checking files in ?vignettes? ... OK * checking examples ... [14s/16s] OK * checking for unstated dependencies in ?tests? ... OK * checking tests ... ERROR Running the tests in ?tests/test-all.R? failed. Last 13 lines of output: 7: with_sink(temp, withCallingHandlers(withVisible(code), warning = wHandler, message = mHandler)) 8: withCallingHandlers(withVisible(code), warning = wHandler, message = mHandler) 9: withVisible(code) 10: disaggregate(data.max.test2) 11: stop(paste("The number of transitions annotated and measured do not match in the following transitions:\n", paste(unlist(n.transitions[n.transitions2 != n.transitions4]), collapse = ", "))) testthat results ================================================================ OK: 46 SKIPPED: 0 FAILED: 1 1. Error: data conversion Error: testthat unit tests failed Execution halted * 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 ERROR, 1 NOTE Hope this helps, Brian ?