Our package ?trena? has had build errors these last two weeks. I have not yet been able to reproduce them on a macOS laptop. Would it be sensible to get the latest release and devel docker images for Bioconductor? Are they similar enough to the build system to give me good odds on reproducing the errors seen there? - Paul
[Bioc-devel] use bioc docker images to reproduce linux build error?
4 messages · Obenchain, Valerie, Paul Shannon
1 day later
Hi Paul, I can reproduce the error on my Linux system but not on the Mac and am not sure why this is. Haven't tried Windows yet but from the looks of the build report that one is fine too. R CMD check on Linux is failing on this line in getRegulatoryRegions,HumanDHSFilter-method: db <- dbConnect(driver, user = user, host = host, dbname = dbname) Does this need a password (and probably DBI::dbConnect for completeness)? There is a similar line in getEncodeRegulatoryTableNames,HumanDHSFilter-method which isn't failing R CMD check because the man page example is wrapped in /dontrun but it does fail for me when run manually. I think this one may also need a password - if you want to give me one off-line I can test this theory. db <- DBI::dbConnect(driver, user = user, host = host, dbname = dbname) I see a .BBSoptions in trena for exclusion on Windows. The reason it's not being respected is because it's malformed and needs a space after the comma between the platforms. Just curious, what was the reason for excluding this on Windows? Val
On 11/15/18 9:23 AM, Paul Shannon wrote:
Our package ?trena? has had build errors these last two weeks. I have not yet been able to reproduce them on a macOS laptop. Would it be sensible to get the latest release and devel docker images for Bioconductor? Are they similar enough to the build system to give me good odds on reproducing the errors seen there? - Paul
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If you want to excluded trena from both 32-bit and 64-bit Windows the better .BBSoption is 'win' instead of both 'win32' and 'win64'. Right now it's skipping 32-bit but executing 64-bit. Val
On 11/16/18 3:04 PM, Obenchain, Valerie wrote:
Hi Paul,
I can reproduce the error on my Linux system but not on the Mac and am
not sure why this is. Haven't tried Windows yet but from the looks of
the build report that one is fine too.
R CMD check on Linux is failing on this line in
getRegulatoryRegions,HumanDHSFilter-method:
db <- dbConnect(driver, user = user, host = host, dbname = dbname)
Does this need a password (and probably DBI::dbConnect for completeness)?
There is a similar line in
getEncodeRegulatoryTableNames,HumanDHSFilter-method which isn't failing
R CMD check because the man page example is wrapped in /dontrun but it
does fail for me when run manually. I think this one may also need a
password - if you want to give me one off-line I can test this theory.
db <- DBI::dbConnect(driver, user = user, host = host, dbname = dbname)
I see a .BBSoptions in trena for exclusion on Windows. The reason it's
not being respected is because it's malformed and needs a space after
the comma between the platforms. Just curious, what was the reason for
excluding this on Windows?
Val
On 11/15/18 9:23 AM, Paul Shannon wrote:
Our package ?trena? has had build errors these last two weeks. I have not yet been able to reproduce them on a macOS laptop. Would it be sensible to get the latest release and devel docker images for Bioconductor? Are they similar enough to the build system to give me good odds on reproducing the errors seen there? - Paul
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1 day later
Hi Val, Thanks for the pointer. I now import RMariaDB in the NAMESPACE and the DESCRIPTION files. That seemed to solve the problem. When I updated from RMySQL, I failed to do that. I changed .BBSoptions to simply ?win? as you suggest, but just as a temporary measure. I don?t remember why we excluded the windows build - perhaps that is not necessary any more. After the package builds clean on macOS and linux, I will experiment with removing the win exclusions. Thank you! - Paul
On Nov 16, 2018, at 3:04 PM, Obenchain, Valerie <Valerie.Obenchain at RoswellPark.org> wrote: Hi Paul, I can reproduce the error on my Linux system but not on the Mac and am not sure why this is. Haven't tried Windows yet but from the looks of the build report that one is fine too. R CMD check on Linux is failing on this line in getRegulatoryRegions,HumanDHSFilter-method: db <- dbConnect(driver, user = user, host = host, dbname = dbname) Does this need a password (and probably DBI::dbConnect for completeness)? There is a similar line in getEncodeRegulatoryTableNames,HumanDHSFilter-method which isn't failing R CMD check because the man page example is wrapped in /dontrun but it does fail for me when run manually. I think this one may also need a password - if you want to give me one off-line I can test this theory. db <- DBI::dbConnect(driver, user = user, host = host, dbname = dbname) I see a .BBSoptions in trena for exclusion on Windows. The reason it's not being respected is because it's malformed and needs a space after the comma between the platforms. Just curious, what was the reason for excluding this on Windows? Val On 11/15/18 9:23 AM, Paul Shannon wrote:
Our package ?trena? has had build errors these last two weeks. I have not yet been able to reproduce them on a macOS laptop. Would it be sensible to get the latest release and devel docker images for Bioconductor? Are they similar enough to the build system to give me good odds on reproducing the errors seen there? - Paul
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This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.