Perhaps it is not obvious to you, but it is fairly obvious to me that the R code in this code chunk is incomplete:
<<>>= xyplot(value ~ sampdate | variable, data=carlin.2.melt, rm.na = T, ylab = 'Measured Value', xlab = 'Date' @ There is a ')' missing in the end. When you see errors from parse(), that often means the code is not syntactically correct. Regards, Yihui -- Yihui Xie <xieyi...@gmail.com> Web: http://yihui.name On Sat, Jul 11, 2015 at 7:07 PM, Rich Shepard <rshep...@appl-ecosys.com> wrote: > On Sat, 11 Jul 2015, Yihui Xie wrote: > >> I guess you didn't tell us you were compiling the document with dvips > > > That's how I preview lyx docs for the past decade-and-a-half or so. The > final .pdf is generated with pdflatex. > > There is now an issue when a second figure is added to the document: it > won't compile. > > Attached are the .RData file from the cwd, the test.lyx file (lyx-2.1.3), > and the two test files from /tmp/.../lyx_tmpbuf3/. > > Here are the lyx messages when I tried compiling the document with > pdflatex: > > 16:51:11.255: Exporting ... > 16:51:11.259: (buffer-export pdf2) > 16:51:11.278: Rscript --verbose --no-save --no-restore > "/usr/share/lyx/scripts/lyxknitr.R" > "/tmp/lyx_tmpdir.rGQZdOZ30938/lyx_tmpbuf3/""test.Rnw" > "/tmp/lyx_tmpdir.rGQZdOZ30938/lyx_tmpbuf3/""test.tex" ISO-8859-15 > "/home/rshepard/documents/white-papers/water-chem-anal/" > 16:51:11.281: running > 16:51:11.286: '/usr/lib/R/bin/R --slave --no-restore --no-save > --no-restore --file=/usr/share/lyx/scripts/lyxknitr.R --args > -- /tmp/lyx_tmpdir.rGQZdOZ30938/lyx_tmpbuf3/test.Rnw > -- / /tmp/lyx_tmpdir.rGQZdOZ30938/lyx_tmpb > 16:51:11.288: uf3/test.tex ISO-8859-15 > /home/rshepard/documents/white-papers/water-chem-anal/' > 16:51:11.292: 16:51:11.697: Loading required package: methods > 16:51:11.709: Loading required package: survival > 16:51:11.712: Loading required package: graphics > 16:51:11.721: Loading required package: stats > 16:51:11.921: 16:51:11.923: Attaching package: ‘NADA’ > 16:51:11.925: 16:51:11.927: The following object is masked from > ‘package:stats’: > 16:51:11.929: 16:51:11.932: cor > 16:51:11.933: 16:51:11.969: 16:51:11.970: Attaching package: ‘zoo’ > 16:51:11.972: 16:51:11.975: The following objects are masked from > ‘package:base’: > 16:51:11.976: 16:51:11.979: as.Date, as.Date.numeric > 16:51:11.981: 16:51:12.091: 16:51:12.092: 16:51:12.094: processing file: > /tmp/lyx_tmpdir.rGQZdOZ30938/lyx_tmpbuf3/test.Rnw > 16:51:12.112: > | > | | 0% > | 16:51:12.113: > |.... | 6% > 16:51:12.116: ordinary text without R code > 16:51:12.118: 16:51:12.120: > | > |........ | 12% > 16:51:12.123: label: unnamed-chunk-1 (with options) 16:51:12.126: List of 1 > 16:51:12.128: $ echo: logi FALSE > 16:51:12.130: 16:51:12.204: > | > |........... | 18% > 16:51:12.205: ordinary text without R code > 16:51:12.207: 16:51:12.210: > | > |............... | 24% > 16:51:12.213: label: unnamed-chunk-2 > 16:51:12.239: > | > |................... | 29% > 16:51:12.240: ordinary text without R code > 16:51:12.242: 16:51:12.244: > | > |....................... | 35% > 16:51:12.247: label: unnamed-chunk-3 > 16:51:12.293: > | > |........................... | 41% > 16:51:12.295: ordinary text without R code > 16:51:12.297: 16:51:12.299: > | > |............................... | 47% > 16:51:12.302: label: unnamed-chunk-4 > 16:51:12.344: > | > |.................................. | 53% > 16:51:12.346: ordinary text without R code > 16:51:12.348: 16:51:12.350: > | > |...................................... | 59% > 16:51:12.353: label: unnamed-chunk-5 > 16:51:12.432: > | > |.......................................... | 65% > 16:51:12.434: ordinary text without R code > 16:51:12.436: 16:51:12.438: > | > |.............................................. | 71% > 16:51:12.441: label: unnamed-chunk-6 > 16:51:12.484: > | > |.................................................. | 76% > 16:51:12.486: ordinary text without R code > 16:51:12.488: 16:51:12.490: > | > |...................................................... | 82% > 16:51:12.493: label: unnamed-chunk-7 > 16:51:12.837: > | > |......................................................... | 88% > 16:51:12.839: ordinary text without R code > 16:51:12.841: 16:51:12.843: > | > |............................................................. | 94% > 16:51:12.846: label: unnamed-chunk-8 > 16:51:12.849: Quitting from lines 101-102 > (/tmp/lyx_tmpdir.rGQZdOZ30938/lyx_tmpbuf3/test.Rnw) 16:51:12.851: Error in > parse(text = x, srcfile = src) : 16:51:12.853: <text>:2:0: unexpected end > of input > 16:51:12.855: 1: xyplot(value ~ sampdate | variable, data=carlin.2.melt, > rm.na = T, ylab = 'Measured Value', xlab = 'Date' > 16:51:12.857: ^ > 16:51:12.859: Calls: knit ... <Anonymous> -> parse_all -> > parse_all.character -> parse > 16:51:12.861: 16:51:12.862: Execution halted > Systemcall.cpp (292): Systemcall: 'Rscript --verbose --no-save --no-restore > "/usr/share/lyx/scripts/lyxknitr.R" > "/tmp/lyx_tmpdir.rGQZdOZ30938/lyx_tmpbuf3/""test.Rnw" > "/tmp/lyx_tmpdir.rGQZdOZ30938/lyx_tmpbuf3/""test.tex" ISO-8859-15 > "/home/rshepard/documents/white-papers/water-chem-anal/"' finished with exit > code 1 > Error: Cannot convert file > ---------------------------------------- > An error occurred while running: > Rscript --verbose --no-save --no-restore "/usr/share/lyx/scripts/lyxknitr.R" > "/tmp/lyx_tmpdir.rGQZdOZ30938/lyx_tmpbuf3/""test.Rnw" > "/tmp/lyx_tmpdir.rGQZdOZ30938/lyx_tmpbuf3/""test.tex" ISO-8859-15 > "/home/rshepard/documents/white-papers/water-chem-anal/" > 16:51:16.136: Error while exporting format: PDF (pdflatex) > > There is no log file in the tempbuf. Note the references to > unnamed-chunks. Each chunk is labeled with a number when opened in lyx; the > two figures each have a distinct label. I don't see the specific error > generated by adding a second figure to the document. If there are more files > needed to reproduce this situation, let me know and I'll provide it. > > Rich ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
