Package: netDx.examples

Version: 0.99.3

Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:netDx.examples.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings netDx.examples_0.99.3.tar.gz

StartedAt: 2020-02-20 14:12:52 -0500 (Thu, 20 Feb 2020)

EndedAt: 2020-02-20 14:14:28 -0500 (Thu, 20 Feb 2020)

EllapsedTime: 96.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: netDx.examples.Rcheck

Warnings: 1

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:netDx.examples.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings netDx.examples_0.99.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-data-experiment/meat/netDx.examples.Rcheck’
* using R Under development (unstable) (2020-01-28 r77731)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netDx.examples/DESCRIPTION’ ... OK
* this is package ‘netDx.examples’ version ‘0.99.3’
* 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 ... NOTE
Found the following non-portable file paths:
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVENO/tmp/BILE_SALT_AND_ORGANIC_ANION_SLC_TRANSPORTERS.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVENO/tmp/CLASS_C_3__METABOTROPIC_GLUTAMATE_PHEROMONE_RECEPTORS_.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVENO/tmp/INCRETIN_SYNTHESIS,_SECRETION,_AND_INACTIVATION.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVENO/tmp/METABOLISM_OF_WATER-SOLUBLE_VITAMINS_AND_COFACTORS.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVENO/tmp/PLATELET_ADHESION_TO_EXPOSED_COLLAGEN.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVENO/tmp/POU5F1__OCT4_,_SOX2,_NANOG_ACTIVATE_GENES_RELATED_TO_PROLIFERATION.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVENO/tmp/REACTIONS_SPECIFIC_TO_THE_COMPLEX_N-GLYCAN_SYNTHESIS_PATHWAY.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVENO/tmp/SIGNALING_EVENTS_MEDIATED_BY_HDAC_CLASS_II.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVENO/tmp/SIGNALING_EVENTS_MEDIATED_BY_HDAC_CLASS_III.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVENO/tmp/SUPERPATHWAY_OF_CHOLESTEROL_BIOSYNTHESIS.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVENO/tmp/SYNTHESIS,_SECRETION,_AND_INACTIVATION_OF_GLUCAGON-LIKE_PEPTIDE-1__GLP-1_.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVENO/tmp/SYNTHESIS,_SECRETION,_AND_INACTIVATION_OF_GLUCOSE-DEPENDENT_INSULINOTROPIC_POLYPEPTIDE__GIP_.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVENO/tmp/SYNTHESIS_OF_LEUKOTRIENES__LT__AND_EOXINS__EX_.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVENO/tmp/TNFR1-INDUCED_PROAPOPTOTIC_SIGNALING.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVENO/tmp/VITAMIN_B5__PANTOTHENATE__METABOLISM.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/ACTIVATION_OF_GENE_EXPRESSION_BY_SREBF__SREBP_.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/ACTIVATION_OF_THE_PRE-REPLICATIVE_COMPLEX.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/COOPERATION_OF_PREFOLDIN_AND_TRIC_CCT_IN_ACTIN_AND_TUBULIN_FOLDING.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/DEFECTS_IN_COBALAMIN__B12__METABOLISM.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/EXPORT_OF_VIRAL_RIBONUCLEOPROTEINS_FROM_NUCLEUS.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/METABOLISM_OF_FOLATE_AND_PTERINES.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/N-GLYCAN_TRIMMING_IN_THE_ER_AND_CALNEXIN_CALRETICULIN_CYCLE.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/NUCLEAR_PORE_COMPLEX__NPC__DISASSEMBLY.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/PLATELET_ADHESION_TO_EXPOSED_COLLAGEN.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/REACTIONS_SPECIFIC_TO_THE_COMPLEX_N-GLYCAN_SYNTHESIS_PATHWAY.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/REGULATION_OF_CHOLESTEROL_BIOSYNTHESIS_BY_SREBP__SREBF_.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/REGULATION_OF_PYRUVATE_DEHYDROGENASE__PDH__COMPLEX.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/RIP-MEDIATED_NFKB_ACTIVATION_VIA_ZBP1.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/TAK1_ACTIVATES_NFKB_BY_PHOSPHORYLATION_AND_ACTIVATION_OF_IKKS_COMPLEX.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/TRANSPORT_OF_MATURE_MRNAS_DERIVED_FROM_INTRONLESS_TRANSCRIPTS.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRONLESS_TRANSCRIPT.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/VITAMIN_B5__PANTOTHENATE__METABOLISM.profile
  netDx.examples/inst/extdata/KIRC_output/rng1/SURVIVEYES/tmp/ZBP1_DAI__MEDIATED_INDUCTION_OF_TYPE_I_IFNS.profile

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘netDx.examples’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 61.8Mb
  sub-directories of 1Mb or more:
    data     29.7Mb
    extdata  32.0Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... 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 Rd files ... NOTE
prepare_Rd: KIRC_dat.Rd:11-13: Dropping empty section \source
prepare_Rd: KIRC_group.Rd:11-13: Dropping empty section \source
prepare_Rd: KIRC_pheno.Rd:11-13: Dropping empty section \source
prepare_Rd: MB.pheno.Rd:10: Dropping empty section \usage
prepare_Rd: MB.xpr_names.Rd:11-12: Dropping empty section \usage
prepare_Rd: TCGA_BRCA.Rd:13: Dropping empty section \usage
prepare_Rd: pheno.Rd:11: Dropping empty section \usage
prepare_Rd: xpr.Rd:11: Dropping empty section \usage
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                 old_size new_size compress
  KIRC_dat.rda      285Kb    230Kb       xz
  KIRC_group.rda    261Kb    148Kb       xz
  MBlastoma.rda     3.1Mb    2.1Mb    bzip2
  TCGA_BRCA.rda    25.1Mb   14.4Mb       xz
  genes.rda         864Kb    664Kb       xz
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-data-experiment/meat/netDx.examples.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL netDx.examples
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘netDx.examples’ ...
** using staged installation
** data
** inst
** help
*** installing help indices
** building package indices
** 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 (netDx.examples)

name	user	system	elapsed
KIRC_dat	0.160	0.104	0.264
KIRC_group	0.231	0.144	0.374
KIRC_pheno	0.005	0.000	0.005
MB.pheno	0.074	0.008	0.082
MB.xpr	0.092	0.008	0.100
MB.xpr_names	0.074	0.000	0.074
TCGA_BRCA	2.676	0.096	2.773
cnv_GR	0.606	0.020	0.626
genes	0.093	0.002	0.096
pheno	0.359	0.010	0.369
xpr	0.433	0.000	0.434