One of your cell files is funky
colSums(exprs(alldata) == 0)
GSM907854.CEL.gz GSM907866.CEL.gz GSM907857.CEL.gz GSM907863.CEL.gz
0 0 0 686388
GSM907856.CEL.gz GSM907862.CEL.gz GSM907855.CEL.gz GSM907861.CEL.gz
0 0 0 0
and it's tickling a bug in preprocessCore
$ R -d gdb -f testOligo.R
...
0x00007fffe190418a in max_density (z=0x7fffcc0008c0, rows=0, cols=1,
column=0)
at rma_background4.c:128
128 rma_background4.c: No such file or dire
(gdb) dir /home/mtmorgan/b/git/preprocessCore/src/
Source directories searched:
/home/mtmorgan/b/git/preprocessCore/src:$cdir:$cwd
(gdb) l
123
124 max_y = find_max(dens_y,16384);
125
126 i = 0;
127 do {
128 if (dens_y[i] == max_y)
129 break;
130 i++;
131
132 } while(1);
(gdb) p i
$1 = 1821306
(gdb) p max_y
Maybe one of the preprocessCore pros will chime in...
Martin
On 05/14/2018 09:15 AM, Joris Meys wrote:
Dear all,
sorry for the delayed response, due to some unfortunate events I had
to
prioritize my family the past week.
You find an RStudio project in a zipped folder on this link :
https://jorismeys.stackstorage.com/s/3ik0vMwsvueuT5a
It contains a script called testOligo.R that can be sourced and nukes
my R
session in the second step of the rma() function. It also contains the
faulty .gz files. If you need more information, don't hesitate to
contact
me.
Regarding improving general maintainability, I'm willing to help out
on
that. Problem is that I'm rather behind with my own work, so I'm short
on
time for the moment. I'll fork affy tomorrow (need to give class now)
and
let's start from there then?
Cheers
Joris
On Sat, May 5, 2018 at 5:17 PM, Vincent Carey
<stvjc at channing.harvard.edu>
wrote:
How about a google drive? This problem of autodownloading should be
addressed directly.
These facilities are still important but their maintenance is clearly
a
lower priority as the
technologies handled have diminished use in the field. I think we
should
be able to team up and remove autoinstallation elements of these
packages,
and
perhaps improve general maintainability -- Joris, can you pick
one, make a github repo that we can collaborate on revising, and then
we can start? It will involve a deprecation process.
On Sat, May 5, 2018 at 10:54 AM, Joris Meys <jorismeys at gmail.com>
wrote:
Thank you for the answer.
I was trying to create a reproducible example before I vented maybe
a bit
too much in my previous mail.
I managed to get closer to the problem and it is related to data
that was
corrupted at download. I can send you a reproducible example that
bombs R,
but I will have to send the specific data files as well. How do I
send
them
best?
Cheers
Joris
On Sat, 5 May 2018, 00:09 James W. MacDonald, <jmacdon at uw.edu>
wrote:
I think there are multiple complaints here, so I'll take them one
at a
time.
On Fri, May 4, 2018 at 3:56 PM, Obenchain, Valerie <
Valerie.Obenchain at roswellpark.org> wrote:
Joris,
Sorry I don't have much to offer here. I've cc'd the authors of
oligo
affy who may have some insight.
Valerie
On 05/02/2018 11:35 AM, Joris Meys wrote:
Dear,
I've noticed that using certain functions in affy and oligo (eg
oligo::read.celfiles and affy::bg.correct) start with downloading
package and end with either R crashing or a warning that -after
installation succeeded- the package is not available.
This is true for oligo, and perhaps a bit annoying. If you don't
have
package installed already, it gets the package, installs it, and
then
it's not available. This is an easy enough fix.
After which using
some functions of both packages still crash R.
I don't know what to do with that. What functions?
The warning I get when trying oligo::read.celfiles() on a single
CEL
right after installing it about the pd.hugene.1.0.st.v1 package.
The
more annoying thing is that on my machine it insists on building
from
source, whereas on another Windows machine without Rtools, it
That is an options setting that gets changed when you install
Rtools.
'pkgType' option gets set to 'both' because you can now install
both
And in install.packages it ends up getting switched from 'both' to
'source'. I haven't dug any further into that because I am not sure
I
why it's a problem. In the end there isn't a difference between
a source or a binary pdInfoPackage, and trying to get it to 'do the
thing' might have some unforeseen consequences that I would rather
not
to worry about. This is really an 'if it ain't broke, don't fix it'
scenario, IMO.
Reason it frustrates the heck out of me, is that both affy and
oligo
crashed the R session in different ways. During installation of a
during use of a function, and at different points when comparing
my
machine
with the one of our students. The culprit seems to be in one of
the
underlying packages, but I wasn't even able to detect which
package is
culprit, let alone which function crashes everything.
I understand your frustration, but that's not enough to go on. I
have
never, in like 18 years, had either oligo or affy randomly segfault
on
I understand that it is happening for you, but unless you can come
up
a reproducible example, it's not possible for anybody to help.
Is there a way around this so I can ensure that at least I have
the
setup as they have and I can try to come up with a reproducible
report this critical bug?
Again, I am not sure what to do with that. I am not sure what 'a
way
around this' pertains to, and ensuring you have the same setup as
'they
have' seems to be something only you can accomplish. Is there some
you cannot ensure that you have the same setup on two different
Thank you in advance
Joris
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