##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:AnnotationForge.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings AnnotationForge_1.49.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/AnnotationForge.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘AnnotationForge/DESCRIPTION’ ... OK
* this is package ‘AnnotationForge’ version ‘1.49.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AnnotationForge’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    AnnDbPkg-templates   1.8Mb
    extdata              3.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’
  ‘GenomeInfoDb:::lookup_organism_by_tax_id’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AnnDbPkg-maker.Rd: AnnDbPkg-checker
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...Fatal error: cannot create 'R_TempDir'
 ERROR
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ...Warning in dir.create(tdir) :
  cannot create dir '/tmp/Rtmp8pzATG/file2521fe7477e168', reason 'No space left on device'
Warning in dir.create(tdir) :
  cannot create dir '/tmp/Rtmp8pzATG/file2521fe6c555045', reason 'No space left on device'
Warning in dir.create(tdir) :
  cannot create dir '/tmp/Rtmp8pzATG/file2521fe1c990307', reason 'No space left on device'
Warning in dir.create(tdir) :
  cannot create dir '/tmp/Rtmp8pzATG/file2521fe69c4dabd', reason 'No space left on device'
 OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
Fatal error: cannot create 'R_TempDir'

* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm ... looks like a package
Converting parsed Rd's to LaTeX .
Creating pdf output from LaTeX ...
This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./Rd2.tex
LaTeX2e <2023-11-01> patch level 1
L3 programming layer <2024-01-22>

(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2023/05/17 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/rapidbuild/bbs-3.21-bioc-rapid/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty)
(/usr/share/texlive/texmf-dist/tex/latex/jknapltx/mathrsfs.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
No file Rd2.aux.
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/share/texlive/texmf-dist/tex/latex/jknapltx/ursfs.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf-dist/fonts/enc/dvips
/base/8r.enc}]
No file Rd2.toc.
[2] [3]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 224--224
 []\T1/pcr/m/n/10 getProbeDataAffy(arraytype, datafile, pkgname = NULL, compare
withcdf = FALSE) 
[4] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [5] [6]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 405--405
 []  \T1/pcr/m/n/9 ## (Note that in this case makeAnnDbPkg() will use the packa
ge descriptions[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 417--417
 []  \T1/pcr/m/n/9 ## Extra args can be used to narrow down the roaster of pack
ages to make:[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 419--419
 []      \T1/pcr/m/n/9 makeAnnDbPkg("", PkgTemplate="HUMANCHIP.DB", manufacture
r="Affymetrix")[] 
[7] [8]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 543--543
 []\T1/pcr/m/n/10 #  makeDBPackage(schema, affy, prefix, fileName, baseMapType,
 version)[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 546--546
 []\T1/pcr/m/n/10 #  makeDBPackage(schema, affy, prefix, fileName, otherSrc, ch
ipMapSrc,[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 547--547
 []\T1/pcr/m/n/10 #  chipSrc, baseMapType, outputDir, version, manufacturer, ch
ipName,[] 
[9]
Overfull \hbox (79.98035pt too wide) in paragraph at lines 633--633
 []    \T1/pcr/m/n/9 fileName = "~/proj/mcarlson/sqliteGen/srcFiles/hgu95av2/HG
_U95Av2_annot.csv.070824",[] 

Overfull \hbox (36.7804pt too wide) in paragraph at lines 636--636
 []        \T1/pcr/m/n/9 UMICH="~/proj/mcarlson/sqliteGen/srcFiles/hgu95av2/hgu
95av2_UMICH.txt"),[] 
[10]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 687--687
 []        \T1/pcr/m/n/9 dir="http://inparanoid.sbc.su.se/download/current/Orth
ologs/A.aegypti/",[] 
[11]
Overfull \hbox (1.25764pt too wide) in paragraph at lines 718--728
\T1/ptm/m/n/10 be named. Those names will be-come the names of the ta-bles in t
he fi-nal database.
[12]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 767--767
 []\T1/pcr/m/n/9 finchFile <- system.file("extdata","finch_info.txt",package="A
nnotationForge")[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 770--770
 []\T1/pcr/m/n/9 ## not that this is how it should always be, but that it *coul
d* be this way.[] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 780--780
 []\T1/pcr/m/n/9 finchGOFile <- system.file("extdata","GO_finch.txt",package="A
nnotationForge")[] 
[13]
Overfull \hbox (11.88753pt too wide) in paragraph at lines 864--868
\T1/ptm/m/n/10 NCBI.sqlite DB and fi-nal pack-age are re-generated from lo-cal 
files in []\T1/pcr/m/n/10 outputDir[]\T1/ptm/m/n/10 .

Overfull \hbox (50.79723pt too wide) in paragraph at lines 878--884
[]\T1/pcr/m/n/10 makeOrgPackageFromNCBI []\T1/ptm/m/n/10 down-loads mul-ti-ple 
files and as-sem-bles a 33 GB database in []\T1/pcr/m/n/10 NCBIFilesDir[]\T1/pt
m/m/n/10 .
[14]
Overfull \hbox (78.76956pt too wide) in paragraph at lines 895--897
[]\T1/ptm/m/n/10 Some orgDbs are al-ready pro-vided through []\T1/pcr/m/n/10 An
notationHub[]\T1/ptm/m/n/10 . See pack-age []\T1/pcr/m/n/10 AnnotationHub::Anno
tationHub 
[15]
Overfull \hbox (5.33826pt too wide) in paragraph at lines 961--963
[]\T1/ptm/m/n/10 Character. Name of the pack-age. If miss-ing, a name is cre-at
ed from []\T1/pcr/m/n/10 arraytype[]\T1/ptm/m/n/10 . 

Overfull \hbox (30.14833pt too wide) in paragraph at lines 967--969
[]\T1/ptm/m/n/10 Logical. If []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 un-link (re
-move) the []\T1/pcr/m/n/10 check []\T1/ptm/m/n/10 di-rec-tory (only rel-e-vant
 if []\T1/pcr/m/n/10 check=TRUE[]\T1/ptm/m/n/10 ) 
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) [16]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1043--1043
 []\T1/pcr/m/n/10 #  populateDB(schema, affy, prefix, fileName, chipMapSrc, chi
pSrc,[] 

Overfull \hbox (0.26762pt too wide) in paragraph at lines 1082--1085
[]\T1/ptm/m/n/10 Either a named char-ac-ter vec-tor con-tain-ing per-ti-nent in
-for-ma-tion about the meta-
[17]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1139--1139
 []    \T1/pcr/m/n/9 chipSrc = "~/proj/mcarlson/sqliteGen/annosrc/db/chipsrc_hu
man.sqlite",[] 

Overfull \hbox (69.18036pt too wide) in paragraph at lines 1149--1149
 []      \T1/pcr/m/n/9 fileName="~/proj/mcarlson/sqliteGen/srcFiles/hgu95av2/HG
_U95Av2.na27.annot.csv",[] 

Overfull \hbox (47.58038pt too wide) in paragraph at lines 1166--1166
 []      \T1/pcr/m/n/9 fileName="~/proj/mcarlson/sqliteGen/srcFiles/yeast2/Yeas
t_2.na27.annot.csv",[] 
[18]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1207--1207
 []  \T1/pcr/m/n/9 ##Make all of the intermediate DBs and place the new package
s right here.[] 
[19] (./Rd2.aux)

Package rerunfilecheck Warning: File `Rd2.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.

 )
(see the transcript file for additional information)
pdfTeX warning (dest): name{Rfn.AnnDbPkg.Rdash.checker} has been referenced but
 does not exist, replaced by a fixed one


pdfTeX warning (dest): name{Rfn.createPackage} has been referenced but does not
 exist, replaced by a fixed one

</usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf
-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/ut
mr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (19 pages, 122395 bytes).
Transcript written on Rd2.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./Rd2.tex
LaTeX2e <2023-11-01> patch level 1
L3 programming layer <2024-01-22>

(/usr/share/texlive/texmf-dist/tex/latex/base/book.cls
Document Class: book 2023/05/17 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo))
(/home/rapidbuild/bbs-3.21-bioc-rapid/R/share/texmf/tex/latex/Rd.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty)
(/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty)
(/usr/share/texlive/texmf-dist/tex/latex/jknapltx/mathrsfs.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty
(/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty)
(/usr/share/texlive/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty)
(/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)
(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty
(/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/etoolbox/etoolbox.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty
(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty
(/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
(./Rd2.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (./Rd2.out) (./Rd2.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)
(/usr/share/texlive/texmf-dist/tex/latex/jknapltx/ursfs.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf-dist/fonts/enc/dvips
/base/8r.enc}] (./Rd2.toc) [2] [3]
Overfull \hbox (66.78088pt too wide) in paragraph at lines 224--224
 []\T1/pcr/m/n/10 getProbeDataAffy(arraytype, datafile, pkgname = NULL, compare
withcdf = FALSE) 
[4] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [5] [6]
Overfull \hbox (20.58041pt too wide) in paragraph at lines 405--405
 []  \T1/pcr/m/n/9 ## (Note that in this case makeAnnDbPkg() will use the packa
ge descriptions[] 

Overfull \hbox (9.78043pt too wide) in paragraph at lines 417--417
 []  \T1/pcr/m/n/9 ## Extra args can be used to narrow down the roaster of pack
ages to make:[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 419--419
 []      \T1/pcr/m/n/9 makeAnnDbPkg("", PkgTemplate="HUMANCHIP.DB", manufacture
r="Affymetrix")[] 
[7] [8] [9]
Overfull \hbox (24.78088pt too wide) in paragraph at lines 543--543
 []\T1/pcr/m/n/10 #  makeDBPackage(schema, affy, prefix, fileName, baseMapType,
 version)[] 

Overfull \hbox (24.78088pt too wide) in paragraph at lines 546--546
 []\T1/pcr/m/n/10 #  makeDBPackage(schema, affy, prefix, fileName, otherSrc, ch
ipMapSrc,[] 

Overfull \hbox (12.78088pt too wide) in paragraph at lines 547--547
 []\T1/pcr/m/n/10 #  chipSrc, baseMapType, outputDir, version, manufacturer, ch
ipName,[] 
[10]
Overfull \hbox (79.98035pt too wide) in paragraph at lines 633--633
 []    \T1/pcr/m/n/9 fileName = "~/proj/mcarlson/sqliteGen/srcFiles/hgu95av2/HG
_U95Av2_annot.csv.070824",[] 

Overfull \hbox (36.7804pt too wide) in paragraph at lines 636--636
 []        \T1/pcr/m/n/9 UMICH="~/proj/mcarlson/sqliteGen/srcFiles/hgu95av2/hgu
95av2_UMICH.txt"),[] 
[11]
Overfull \hbox (36.7804pt too wide) in paragraph at lines 687--687
 []        \T1/pcr/m/n/9 dir="http://inparanoid.sbc.su.se/download/current/Orth
ologs/A.aegypti/",[] 

Overfull \hbox (1.25764pt too wide) in paragraph at lines 718--728
\T1/ptm/m/n/10 be named. Those names will be-come the names of the ta-bles in t
he fi-nal database.
[12]
Overfull \hbox (25.98041pt too wide) in paragraph at lines 767--767
 []\T1/pcr/m/n/9 finchFile <- system.file("extdata","finch_info.txt",package="A
nnotationForge")[] 

Overfull \hbox (20.58041pt too wide) in paragraph at lines 770--770
 []\T1/pcr/m/n/9 ## not that this is how it should always be, but that it *coul
d* be this way.[] 

Overfull \hbox (25.98041pt too wide) in paragraph at lines 780--780
 []\T1/pcr/m/n/9 finchGOFile <- system.file("extdata","GO_finch.txt",package="A
nnotationForge")[] 
[13]
Overfull \hbox (11.88753pt too wide) in paragraph at lines 864--868
\T1/ptm/m/n/10 NCBI.sqlite DB and fi-nal pack-age are re-generated from lo-cal 
files in []\T1/pcr/m/n/10 outputDir[]\T1/ptm/m/n/10 .

Overfull \hbox (50.79723pt too wide) in paragraph at lines 878--884
[]\T1/pcr/m/n/10 makeOrgPackageFromNCBI []\T1/ptm/m/n/10 down-loads mul-ti-ple 
files and as-sem-bles a 33 GB database in []\T1/pcr/m/n/10 NCBIFilesDir[]\T1/pt
m/m/n/10 .
[14]
Overfull \hbox (78.76956pt too wide) in paragraph at lines 895--897
[]\T1/ptm/m/n/10 Some orgDbs are al-ready pro-vided through []\T1/pcr/m/n/10 An
notationHub[]\T1/ptm/m/n/10 . See pack-age []\T1/pcr/m/n/10 AnnotationHub::Anno
tationHub 
[15]
Overfull \hbox (5.33826pt too wide) in paragraph at lines 961--963
[]\T1/ptm/m/n/10 Character. Name of the pack-age. If miss-ing, a name is cre-at
ed from []\T1/pcr/m/n/10 arraytype[]\T1/ptm/m/n/10 . 

Overfull \hbox (30.14833pt too wide) in paragraph at lines 967--969
[]\T1/ptm/m/n/10 Logical. If []\T1/pcr/m/n/10 TRUE []\T1/ptm/m/n/10 un-link (re
-move) the []\T1/pcr/m/n/10 check []\T1/ptm/m/n/10 di-rec-tory (only rel-e-vant
 if []\T1/pcr/m/n/10 check=TRUE[]\T1/ptm/m/n/10 ) 
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) [16]
Overfull \hbox (0.78088pt too wide) in paragraph at lines 1043--1043
 []\T1/pcr/m/n/10 #  populateDB(schema, affy, prefix, fileName, chipMapSrc, chi
pSrc,[] 

Overfull \hbox (0.26762pt too wide) in paragraph at lines 1082--1085
[]\T1/ptm/m/n/10 Either a named char-ac-ter vec-tor con-tain-ing per-ti-nent in
-for-ma-tion about the meta-
[17]
Overfull \hbox (4.38043pt too wide) in paragraph at lines 1139--1139
 []    \T1/pcr/m/n/9 chipSrc = "~/proj/mcarlson/sqliteGen/annosrc/db/chipsrc_hu
man.sqlite",[] 

Overfull \hbox (69.18036pt too wide) in paragraph at lines 1149--1149
 []      \T1/pcr/m/n/9 fileName="~/proj/mcarlson/sqliteGen/srcFiles/hgu95av2/HG
_U95Av2.na27.annot.csv",[] 

Overfull \hbox (47.58038pt too wide) in paragraph at lines 1166--1166
 []      \T1/pcr/m/n/9 fileName="~/proj/mcarlson/sqliteGen/srcFiles/yeast2/Yeas
t_2.na27.annot.csv",[] 
[18]
Overfull \hbox (9.78043pt too wide) in paragraph at lines 1207--1207
 []  \T1/pcr/m/n/9 ##Make all of the intermediate DBs and place the new package
s right here.[] 
[19] (./Rd2.aux) )
(see the transcript file for additional information)
pdfTeX warning (dest): name{Rfn.AnnDbPkg.Rdash.checker} has been referenced but
 does not exist, replaced by a fixed one


pdfTeX warning (dest): name{Rfn.createPackage} has been referenced but does not
 exist, replaced by a fixed one

</usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf
-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/ut
mr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on Rd2.pdf (19 pages, 124389 bytes).
Transcript written on Rd2.log.
Saving output to ‘AnnotationForge-manual.pdf’ ...
Done
You may want to clean up by 'rm -Rf /tmp/Rtmp8pzATG/Rd2pdf2521fe3f0d6f5c'
* DONE

Status: 3 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/AnnotationForge.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL AnnotationForge
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘AnnotationForge’ ...
** this is package ‘AnnotationForge’ version ‘1.49.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (AnnotationForge)