RE: error message from xpose
Hi Mark,
The tidyselect package has recently undergone some significant changes. I
would guess that may have caused an issue with xpose which heavily uses the
tidyverse. As Duy indicated, I’d suggest posting an issue to GitHub so
that Ben can help.
Thanks,
Bill
*From:* [email protected] <[email protected]> *On
Behalf Of *Duy Tran
*Sent:* Friday, February 14, 2020 4:04 PM
*To:* Mark Sale <[email protected]>
*Cc:* [email protected]
*Subject:* Re: [NMusers] error message from xpose
Hi Mark,
Can you try specifying more in the arguments for the function
xpose::xpose_data? I typically include these below when I run xpose on R:
xpdb <- xpose_data(runno = "001", ext = ".lst", prefix = "run", dir = "./
msale/XXX/xpose")
If it doesn't work, can you post this issue on
https://github.com/UUPharmacometrics/xpose/issues for the xpose package
developer to help?
-Duy Tran
Quoted reply history
On Fri, Feb 14, 2020 at 12:41 PM Mark Sale <[email protected]> wrote:
I know this is a NONMEM list server, but, need help with xpose, hope you'll
indulge me. Moving to the latest xpose (from xpose4). I ran a model (using
PSN, execute), model file called run001.mod, the $TABLE records are:
$TABLE ID TIME TAD IPRED IWRES NOPRINT ONEHEADER FILE=sdtab001
$TABLE ID K S2 KA CL ETA1 ETA2 ETA3 NOPRINT NOAPPEND ONEHEADER
FILE=patab001
$TABLE ID STDY SEXN RACEN XXXXX XXXXXX NOPRINT NOAPPEND
ONEHEADER FILE=catab001
$TABLE ID AGE XXXXX XXXXX XXXX XXXXX
NOPRINT NOAPPEND ONEHEADER FILE=cotab001
$TABLE ID TIME DV EVID CWRES IWRES XXXX IPRED NOPRINT NOAPPEND
ONEHEADER FILE=cwtab001
I'm trying to load the data in to xpose, with command:
xpdb <- xpose::xpose_data(runno = '001')
getting this ouput:
Looking for nonmem output tables.
Reading: sdtab001, patab001, catab001, cotab001, cwtab001 [$prob no.1]
Looking for nonmem output files
Reading: run001.ext, run001.phi
Warning messages:
1: No tidyselect variables were registered
2: Failed to create run summary. No tidyselect variables were registered
3: No tidyselect variables were registered
I think all the required files are there:
Volume in drive E is New Volume
Volume Serial Number is CC55-6FD7
Directory of E:\msale\XXX\xpose
02/14/2020 03:23 PM 564,745 catab001
02/14/2020 03:23 PM 731,389 cotab001
02/14/2020 03:23 PM 675,841 cwtab001
02/14/2020 03:23 PM 675,841 patab001
02/14/2020 03:23 PM 14 run001.cpu
02/14/2020 03:23 PM 3,615 run001.ext
02/14/2020 03:23 PM 1,857 run001.log
02/14/2020 03:23 PM 18,201 run001.lst
02/14/2020 03:19 PM 3,620 run001.mod
02/14/2020 03:23 PM 173,746 run001.phi
02/14/2020 03:23 PM 1,197 run001.shk
02/14/2020 03:23 PM 37,664 run001.shm
02/14/2020 03:23 PM 20,400 run001.xml
02/14/2020 03:23 PM 509,197 sdtab001
14 File(s) 3,417,327 bytes
0 Dir(s) 59,120,144,384 bytes free
Base on a search for this error, it looks like it comes from dplyr. I'm
running dplyr version 0.8.4, xpose version 0.4.7 and R version 3.6.2 with R
Studio, under Windows 10.
I've tried it with and without the NOAPPEND in the $TABLE records.
Any suggestions would be appreciated.
Mark Sale M.D.
Senior Vice President, Pharmacometrics
Nuventra Inc.
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[email protected] http://[email protected]
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