Here is what I would do to read your data:
> psAll <- readLines("/temp/node1-ps-1.txt")
> ps <- read.table(text = substring(psAll, 1, 65) # parse the first part
+ , header = TRUE
+ , as.is = TRUE
+ , fill = TRUE
+ , check.names = FALSE
+ )
> commands <- substring(psAll, 66)[-1] # remove header
> ps <- cbind(ps, COMMAND = commands)
>
> head(ps)
USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND
1 root 1 0 0 10372 692 ? Ss Aug09 0:02 init [5]
2 root 2 0 0 0 0 ? S< Aug09 0:00 [migration/0]
3 root 3 0 0 0 0 ? SN Aug09 0:00 [ksoftirqd/0]
4 root 4 0 0 0 0 ? S< Aug09 0:00 [watchdog/0]
5 root 5 0 0 0 0 ? S< Aug09 0:00 [migration/1]
6 root 6 0 0 0 0 ? SN Aug09 0:00 [ksoftirqd/1]
>
On Fri, Aug 16, 2013 at 9:08 AM, <mohan.radhakrish...@polarisft.com> wrote:
> My code is not complete. But the headers I see are
>
> USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND
> 68 4517 0.0 0.0 12348 864 ? S Aug08 0:00
> hald-addon-keyboard: listening on /dev/input/event1
> 68 4521 0.0 0.0 12348 860 ? S Aug08 0:00
> hald-addon-keyboard: listening on /dev/input/event0
> root 4529 0.0 0.0 10256 704 ? S Aug08 1:57
> hald-addon-storage: polling /dev/sr0
>
> The last column value doesn't follow any rule.
>
> Thanks,
> Mohan
>
>
>
>
>
> Re: [R] Output from unix PS
>
>
> Sarah Goslee
> to:
> mohan.radhakrishnan
> 16-08-2013 06:01 PM
>
>
>
>
> Cc:
> r-help
>
>
>
>
>
>
>
>
>
> You don't tell us your OS details or provide an actual reproducible
> example, but the error suggests that COMMAND is not one of the column
> names in your data frame.
>
> Have you checked that? When I run ps on my Fedora system, the column
> name is CMD and not COMMAND.
>
> Sarah
>
> On Fri, Aug 16, 2013 at 7:30 AM, <mohan.radhakrish...@polarisft.com>
> wrote:
> > Hi,
> >
> > When I view this output from the unix command ''ps'' the columns seem to
> > properly aligned but it is not read properly into the data frame. The
> > aggregate function throws
> >
> > Error in aggregate.data.frame(data, by = list(COMMAND), FUN = sum) :
> > object 'COMMAND' not found
> >
> > Is there a recomendation to massage this ?
> >
> > data = read.table("D:\\p..txt",sep="\t")
> >
> > agg<-aggregate(data,by=list(COMMAND),FUN=sum)
> >
> > 68 4524 0.0 0.0 12348 872 ? S Aug09 0:00
> > hald-addon-acpi: listening on acpid socket /var/run/acpid.socket
> > 68 4528 0.0 0.0 12348 860 ? S Aug09 0:00
> > hald-addon-keyboard: listening on /dev/input/event1
> > 68 4532 0.0 0.0 12348 864 ? S Aug09 0:00
> > hald-addon-keyboard: listening on /dev/input/event0
> > root 4540 0.0 0.0 10256 704 ? S Aug09 1:02
> > hald-addon-storage: polling /dev/sr0
> > root 4576 0.0 0.0 8540 492 ? Ss Aug09
> > 0:00 /usr/bin/hidd --server
> > root 4619 0.0 0.0 122008 1540 ? Ssl Aug09 0:00
> automount
> > root 4636 0.0 0.0 26348 524 ? Ss Aug09 0:00 ./hpiod
> > root 4641 0.0 0.0 154876 6428 ? S Aug09
> > 0:00 /usr/bin/python ./hpssd.py
> > root 4654 0.0 0.0 63544 1212 ? Ss Aug09
> > 0:00 /usr/sbin/sshd
> > root 4663 0.0 0.0 134208 2744 ? Ss Aug09 0:00 cupsd
> > root 4677 0.0 0.0 21668 896 ? Ss Aug09 0:00 xinetd
> > -stayalive -pidfile /var/run/xinetd.pid
> > root 4695 0.0 0.0 66968 2324 ? Ss Aug09 0:00
> sendmail:
> > accepting connections
> > smmsp 4703 0.0 0.0 57716 1760 ? Ss Aug09 0:00
> sendmail:
> > Queue runner@01:00:00 for /var/spool/clientmqueue
> > root 4713 0.0 0.0 6480 372 ? Ss Aug09 0:00 gpm
> > -m /dev/input/mice -t exps2
> >
> > Thanks.
> >
> >
> >
> --
> Sarah Goslee
> http://www.functionaldiversity.org
>
>
>
>
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