Trying to upgrade bio3d Debian package
Hi Barry,
as you might know there is a Debian package of bio3d maintained by the
Debian Med team. I just realised that we are really lagging behind your
upstream version which is caused by the fact that the watch file which
regularly checks the download area pointed to an old location. I try to
fix this now. While doing the package upgrade I also want to add code
for a so called autopkgtest which is some mechanism to regularly run the
test suite of Debian packages.
I did:
LC_ALL=C R --no-save <<EOT
library(testthat)
library(bio3d)
test_package("bio3d")
EOT
R version 3.1.0 (2014-04-10) -- "Spring Dance"
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Platform: x86_64-pc-linux-gnu (64-bit)
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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(bio3d)
> test_package("bio3d")
Testing aa2mass() : ...
Testing atom mass functions : .........
Testing dccm.nma : .....
Testing deformation analysis : .....
Testing fitting functions : 1234
Testing get.pdb() : ....Timing stopped at: 0.016 0.036 25.486
5
Testing nma() : .........................
Testing overlap functions : ......
Testing vector functions : ....
1. Error: Fitting still works --------------------------------------------------
An error occurred while running command
'muscle'
1: capture.output(pdbs <- pdbaln(c("1hel", "1dpx", "1h87"))) at test-fitting.R:10
2: evalVis(expr)
3: withVisible(eval(expr, pf))
4: eval(expr, pf)
5: eval(expr, envir, enclos)
6: pdbaln(c("1hel", "1dpx", "1h87"))
7: seqaln(s, id = files, extra.args = "-quiet", ...)
8: stop(paste("An error occurred while running command\n '", exefile, "'", sep = ""))
2. Error: struct.aln still works -----------------------------------------------
An error occurred while running command
'muscle'
1: capture.output(aln <- struct.aln(pdb.a, pdb.b, write.pdbs = FALSE, cutoff = 0.1,
max.cycles = 2, extra.args = "-quiet")) at test-fitting.R:44
2: evalVis(expr)
3: withVisible(eval(expr, pf))
4: eval(expr, pf)
5: eval(expr, envir, enclos)
6: struct.aln(pdb.a, pdb.b, write.pdbs = FALSE, cutoff = 0.1, max.cycles = 2, extra.args = "-quiet")
7: seqaln(s, id = c("fixed", "mobile"), ...)
8: stop(paste("An error occurred while running command\n '", exefile, "'", sep = ""))
3. Error: fit.xyz() gets the same results as VMD -------------------------------
An error occurred while running command
'muscle'
1: capture.output(pdbs <- pdbaln(c("1tag", "1as0"))) at test-fitting.R:59
2: evalVis(expr)
3: withVisible(eval(expr, pf))
4: eval(expr, pf)
5: eval(expr, envir, enclos)
6: pdbaln(c("1tag", "1as0"))
7: seqaln(s, id = files, extra.args = "-quiet", ...)
8: stop(paste("An error occurred while running command\n '", exefile, "'", sep = ""))
4. Error: fit.xyz() with ncore>1 works properly --------------------------------
An error occurred while running command
'muscle'
1: capture.output(pdbs <- pdbaln(c("1tag", "1as0", "1as2"))) at test-fitting.R:75
2: evalVis(expr)
3: withVisible(eval(expr, pf))
4: eval(expr, pf)
5: eval(expr, envir, enclos)
6: pdbaln(c("1tag", "1as0", "1as2"))
7: seqaln(s, id = files, extra.args = "-quiet", ...)
8: stop(paste("An error occurred while running command\n '", exefile, "'", sep = ""))
5. Error: get.pdb() with ncore>1 works properly --------------------------------
could not find function "readChildren"
1: system.time(r2 <- get.pdb(ids, tmp2, ncore = 2, verbose = FALSE)) at test-get.pdb.R:21
2: get.pdb(ids, tmp2, ncore = 2, verbose = FALSE)
Error: Test failures
Execution halted
I can confirm that on the machine running the test /usr/bin/muscle
(version 3.8.31) is installed - so I wonder why muscle is not found,
I also have no idea where to obtain the function readChildren.
Any hint how to successfully run the test?
As a side note: Is there any reason not to use CRAN to distribute
bio3d? This could easily avoid the problem of failing to detect the
latest upstream version and would give bio3d possibly the popularity
it deserves.
Kind regards
Andreas.
--
http://fam-tille.de
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