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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocSet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocSet_1.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BiocSet.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocSet/DESCRIPTION’ ... OK
* this is package ‘BiocSet’ version ‘1.21.0’
* 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 ‘BiocSet’ can be installed ... OK
* checking installed package size ... OK
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
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* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘BiocSet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mapping_set
> ### Title: Functions for mapping sets in the set tibble to different id
> ###   types
> ### Aliases: mapping_set go_sets kegg_sets map_set map_add_set
> 
> ### ** Examples
> 
> library(org.Hs.eg.db)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following object is masked from ‘package:dplyr’:

    explain

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: ‘BiocGenerics’

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    combine

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    IQR, mad, sd, var, xtabs

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    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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    collapse, desc, slice


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    select

> go <- go_sets(org.Hs.eg.db, "ENSEMBL")
'select()' returned 1:many mapping between keys and columns
> 
> kegg_sets("hsa")
Error in if (.self$lastField == "REFERENCE") { : 
  missing value where TRUE/FALSE needed
Calls: kegg_sets ... keggGet -> .getUrl -> do.call -> <Anonymous> -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
BiocSet-methods 10.552  0.812  11.528
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. └─BiocSet::kegg_sets("dme") at test_mapping_set.R:63:5
   2.   └─base::lapply(...)
   3.     └─BiocSet (local) FUN(X[[i]], ...)
   4.       └─KEGGREST::keggGet(x)
   5.         └─KEGGREST:::.getUrl(url, .flatFileParser)
   6.           ├─base::do.call(parser, list(content, ...))
   7.           └─KEGGREST (local) `<fn>`("ENTRY       dme01100          Global    Pathway\nNAME        Metabolic pathways - Drosophila melanogaster (fruit fly)\nPATHWAY_MAP dme01100  Metabolic pathways\nMODULE      dme_M00001  Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate [PATH:dme01100]\n            dme_M00002  Glycolysis, core module involving three-carbon compounds [PATH:dme01100]\n            dme_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:dme01100]\n            dme_M00004  Pentose phosphate pathway (Pentose phosphate cycle) [PATH:dme01100]\n            dme_M00005  PRPP biosynthesis, ribose 5P => PRPP [PATH:dme01100]\n            dme_M00006  Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P [PATH:dme01100]\n            dme_M00007  Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P [PATH:dme01100]\n            dme_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:dme01100]\n            dme_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:dme01100]\n            dme_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:dme01100]\n            dme_M00013  Malonate semialdehyde pathway, propanoyl-CoA => acetyl-CoA [PATH:dme01100]\n            dme_M00014  Glucuronate pathway (uronate pathway) [PATH:dme01100]\n            dme_M00015  Proline biosynthesis, glutamate => proline [PATH:dme01100]\n            dme_M00020  Serine biosynthesis, glycerate-3P => serine [PATH:dme01100]\n            dme_M00027  GABA (gamma-Aminobutyrate) shunt [PATH:dme01100]\n            dme_M00034  Methionine salvage pathway [PATH:dme01100]\n            dme_M00035  Methionine degradation [PATH:dme01100]\n            dme_M00036  Leucine degradation, leucine => acetoacetate + acetyl-CoA [PATH:dme01100]\n            dme_M00044  Tyrosine degradation, tyrosine => homogentisate [PATH:dme01100]\n            dme_M00046  Pyrimidine degradation, uracil => beta-alanine, thymine => 3-aminoisobutanoate [PATH:dme01100]\n            dme_M00048  De novo purine biosynthesis, PRPP + glutamine => IMP [PATH:dme01100]\n            dme_M00049  Adenine ribonucleotide biosynthesis, IMP => ADP,ATP [PATH:dme01100]\n            dme_M00050  Guanine ribonucleotide biosynthesis, IMP => GDP,GTP [PATH:dme01100]\n            dme_M00051  De novo pyrimidine biosynthesis, glutamine (+ PRPP) => UMP [PATH:dme01100]\n            dme_M00052  Pyrimidine ribonucleotide biosynthesis, UMP => UDP/UTP,CDP/CTP [PATH:dme01100]\n            dme_M00053  Deoxyribonucleotide biosynthesis, ADP/GDP/CDP/UDP => dATP/dGTP/dCTP/dUTP [PATH:dme01100]\n            dme_M00057  Glycosaminoglycan biosynthesis, linkage tetrasaccharide [PATH:dme01100]\n            dme_M00058  Glycosaminoglycan biosynthesis, chondroitin sulfate backbone [PATH:dme01100]\n            dme_M00059  Glycosaminoglycan biosynthesis, heparan sulfate backbone [PATH:dme01100]\n            dme_M00073  N-glycan precursor trimming [PATH:dme01100]\n            dme_M00082  Fatty acid biosynthesis, initiation [PATH:dme01100]\n            dme_M00083  Fatty acid biosynthesis, elongation [PATH:dme01100]\n            dme_M00085  Fatty acid elongation in mitochondria [PATH:dme01100]\n            dme_M00086  beta-Oxidation, acyl-CoA synthesis [PATH:dme01100]\n            dme_M00087  beta-Oxidation [PATH:dme01100]\n            dme_M00089  Triacylglycerol biosynthesis [PATH:dme01100]\n            dme_M00092  Phosphatidylethanolamine (PE) biosynthesis, ethanolamine => PE [PATH:dme01100]\n            dme_M00094  Ceramide biosynthesis [PATH:dme01100]\n            dme_M00095  C5 isoprenoid biosynthesis, mevalonate pathway [PATH:dme01100]\n            dme_M00099  Sphingosine biosynthesis [PATH:dme01100]\n            dme_M00100  Sphingosine degradation [PATH:dme01100]\n            dme_M00118  Glutathione biosynthesis, glutamate => glutathione [PATH:dme01100]\n            dme_M00120  Coenzyme A biosynthesis, pantothenate => CoA [PATH:dme01100]\n            dme_M00128  Ubiquinone biosynthesis, eukaryotes, 4-hydroxybenzoate + polyprenyl-PP => ubiquinone [PATH:dme01100]\n            dme_M00130  Inositol phosphate metabolism, PI=> PIP2 => Ins(1,4,5)P3 => Ins(1,3,4,5)P4 [PATH:dme01100]\n            dme_M00131  Inositol phosphate metabolism, Ins(1,3,4,5)P4 => Ins(1,3,4)P3 => myo-inositol [PATH:dme01100]\n            dme_M00134  Polyamine biosynthesis, arginine => ornithine => putrescine [PATH:dme01100]\n            dme_M00141  C1-unit interconversion, eukaryotes [PATH:dme01100]\n            dme_M00142  NADH:ubiquinone oxidoreductase, mitochondria [PATH:dme01100]\n            dme_M00143  NADH dehydrogenase (ubiquinone) Fe-S protein/flavoprotein complex, mitochondria [PATH:dme01100]\n            dme_M00148  Succinate dehydrogenase (ubiquinone) [PATH:dme01100]\n            dme_M00151  Cytochrome bc1 complex respiratory unit [PATH:dme01100]\n            dme_M00154  Cytochrome c oxidase [PATH:dme01100]\n            dme_M00158  F-type ATPase, eukaryotes [PATH:dme01100]\n            dme_M00160  V-type ATPase, eukaryotes [PATH:dme01100]\n            dme_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:dme01100]\n            dme_M00338  Cysteine biosynthesis, homocysteine + serine => cysteine [PATH:dme01100]\n            dme_M00367  C10-C20 isoprenoid biosynthesis, non-plant eukaryotes [PATH:dme01100]\n            dme_M00415  Fatty acid elongation in endoplasmic reticulum [PATH:dme01100]\n            dme_M00549  Nucleotide sugar biosynthesis, glucose => UDP-glucose [PATH:dme01100]\n            dme_M00621  Glycine cleavage system [PATH:dme01100]\n            dme_M00842  Tetrahydrobiopterin biosynthesis, GTP => BH4 [PATH:dme01100]\n            dme_M00854  Glycogen biosynthesis, glucose-1P => glycogen/starch [PATH:dme01100]\n            dme_M00855  Glycogen degradation, glycogen => glucose-6P [PATH:dme01100]\n            dme_M00861  beta-Oxidation, peroxisome, VLCFA [PATH:dme01100]\n            dme_M00868  Heme biosynthesis, animals and fungi, glycine => heme [PATH:dme01100]\n            dme_M00880  Molybdenum cofactor biosynthesis, GTP => molybdenum cofactor [PATH:dme01100]\n            dme_M00882  Lipoic acid biosynthesis, eukaryotes, octanoyl-ACP => dihydrolipoyl-H [PATH:dme01100]\n            dme_M00883  Lipoic acid biosynthesis, animals and bacteria, octanoyl-ACP => dihydrolipoyl-H => dihydrolipoyl-E2 [PATH:dme01100]\n            dme_M00892  UDP-N-acetyl-D-glucosamine biosynthesis, eukaryotes, glucose => UDP-GlcNAc [PATH:dme01100]\n            dme_M00938  Pyrimidine deoxyribonucleotide biosynthesis, UDP => dTTP [PATH:dme01100]\n            dme_M00958  Adenine ribonucleotide degradation, AMP => Urate [PATH:dme01100]\n            dme_M00959  Guanine ribonucleotide degradation, GMP => Urate [PATH:dme01100]\n            dme_M00970  Proline degradation, proline => glutamate [PATH:dme01100]\n            dme_M00972  Proline metabolism [PATH:dme01100]\n            dme_M00983  GPI-anchor remodeling [PATH:dme01100]\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nREL_PATHWAY dme00010  Glycolysis / Gluconeogenesis\n            dme00020  Citrate cycle (TCA cycle)\n            dme00030  Pentose phosphate pathway\n            dme00040  Pentose and glucuronate interconversions\n            dme00051  Fructose and mannose metabolism\n            dme00052  Galactose metabolism\n            dme00053  Ascorbate and aldarate metabolism\n            dme00061  Fatty acid biosynthesis\n            dme00062  Fatty acid elongation\n            dme00071  Fatty acid degradation\n            dme00100  Steroid biosynthesis\n            dme00130  Ubiquinone and other terpenoid-quinone biosynthesis\n            dme00190  Oxidative phosphorylation\n            dme00220  Arginine biosynthesis\n            dme00230  Purine metabolism\n            dme00232  Caffeine metabolism\n            dme00240  Pyrimidine metabolism\n            dme00250  Alanine, aspartate and glutamate metabolism\n            dme00260  Glycine, serine and threonine metabolism\n            dme00270  Cysteine and methionine metabolism\n            dme00280  Valine, leucine and isoleucine degradation\n            dme00290  Valine, leucine and isoleucine biosynthesis\n            dme00310  Lysine degradation\n            dme00330  Arginine and proline metabolism\n            dme00340  Histidine metabolism\n            dme00350  Tyrosine metabolism\n            dme00360  Phenylalanine metabolism\n            dme00380  Tryptophan metabolism\n            dme00400  Phenylalanine, tyrosine and tryptophan biosynthesis\n            dme00410  beta-Alanine metabolism\n            dme00430  Taurine and hypotaurine metabolism\n            dme00440  Phosphonate and phosphinate metabolism\n            dme00450  Selenocompound metabolism\n            dme00470  D-Amino acid metabolism\n            dme00480  Glutathione metabolism\n            dme00500  Starch and sucrose metabolism\n            dme00510  N-Glycan biosynthesis\n            dme00511  Other glycan degradation\n            dme00512  Mucin type O-glycan biosynthesis\n            dme00513  Various types of N-glycan biosynthesis\n            dme00514  Other types of O-glycan biosynthesis\n            dme00515  Mannose type O-glycan biosynthesis\n            dme00520  Amino sugar and nucleotide sugar metabolism\n            dme00531  Glycosaminoglycan degradation\n            dme00532  Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate\n            dme00534  Glycosaminoglycan biosynthesis - heparan sulfate / heparin\n            dme00541  Biosynthesis of various nucleotide sugars\n            dme00561  Glycerolipid metabolism\n            dme00562  Inositol phosphate metabolism\n            dme00563  Glycosylphosphatidylinositol (GPI)-anchor biosynthesis\n            dme00564  Glycerophospholipid metabolism\n            dme00565  Ether lipid metabolism\n            dme00590  Arachidonic acid metabolism\n            dme00592  alpha-Linolenic acid metabolism\n            dme00600  Sphingolipid metabolism\n            dme00601  Glycosphingolipid biosynthesis - lacto and neolacto series\n            dme00603  Glycosphingolipid biosynthesis - globo and isoglobo series\n            dme00604  Glycosphingolipid biosynthesis - ganglio series\n            dme00620  Pyruvate metabolism\n            dme00630  Glyoxylate and dicarboxylate metabolism\n            dme00640  Propanoate metabolism\n            dme00650  Butanoate metabolism\n            dme00670  One carbon pool by folate\n            dme00730  Thiamine metabolism\n            dme00740  Riboflavin metabolism\n            dme00750  Vitamin B6 metabolism\n            dme00760  Nicotinate and nicotinamide metabolism\n            dme00770  Pantothenate and CoA biosynthesis\n            dme00780  Biotin metabolism\n            dme00785  Lipoic acid metabolism\n            dme00790  Folate biosynthesis\n            dme00830  Retinol metabolism\n            dme00860  Porphyrin metabolism\n            dme00900  Terpenoid backbone biosynthesis\n            dme00910  Nitrogen metabolism\n            dme00920  Sulfur metabolism\n            dme00980  Metabolism of xenobiotics by cytochrome P450\n            dme00981  Insect hormone biosynthesis\n            dme00982  Drug metabolism - cytochrome P450\n            dme00983  Drug metabolism - other enzymes\n            dme01040  Biosynthesis of unsaturated fatty acids\nKO_PATHWAY  ko01100\n///\n\nENTRY       dme01200          Overview  Pathway\nNAME        Carbon metabolism - Drosophila melanogaster (fruit fly)\nDESCRIPTION Carbon metabolism is the most basic aspect of life. This map presents an overall view of central carbon metabolism, where the number of carbons is shown for each compound denoted by a circle, excluding a cofactor (CoA, CoM, THF, or THMPT) that is replaced by an asterisk. The map contains carbon utilization pathways of glycolysis (map00010), pentose phosphate pathway (map00030), and citrate cycle (map00020), and six known carbon fixation pathways (map00710 and map00720) as well as some pathways of methane metabolism (map00680). The six carbon fixation pathways are: (1) reductive pentose phosphate cycle (Calvin cycle) in plants and cyanobacteria that perform oxygenic photosynthesis, (2) reductive citrate cycle in photosynthetic green sulfur bacteria and some chemolithoautotrophs, (3) 3-hydroxypropionate bi-cycle in photosynthetic green nonsulfur bacteria, two variants of 4-hydroxybutyrate pathways in Crenarchaeota called (4) hydroxypropionate-hydroxybutyrate cycle and (5) dicarboxylate-hydroxybutyrate cycle, and (6) reductive acetyl-CoA pathway in methanogenic bacteria.\nPATHWAY_MAP dme01200  Carbon metabolism\nMODULE      dme_M00001  Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate [PATH:dme01200]\n            dme_M00002  Glycolysis, core module involving three-carbon compounds [PATH:dme01200]\n            dme_M00004  Pentose phosphate pathway (Pentose phosphate cycle) [PATH:dme01200]\n            dme_M00005  PRPP biosynthesis, ribose 5P => PRPP [PATH:dme01200]\n            dme_M00006  Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P [PATH:dme01200]\n            dme_M00007  Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P [PATH:dme01200]\n            dme_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:dme01200]\n            dme_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:dme01200]\n            dme_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:dme01200]\n            dme_M00013  Malonate semialdehyde pathway, propanoyl-CoA => acetyl-CoA [PATH:dme01200]\n            dme_M00020  Serine biosynthesis, glycerate-3P => serine [PATH:dme01200]\n            dme_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:dme01200]\n            dme_M00621  Glycine cleavage system [PATH:dme01200]\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nKO_PATHWAY  ko01200\n///\n\nENTRY       dme01210          Overview  Pathway\nNAME        2-Oxocarboxylic acid metabolism - Drosophila melanogaster (fruit fly)\nDESCRIPTION 2-Oxocarboxylic acids, also called 2-oxo acids and alpha-keto acids, are the most elementary set of metabolites that includes pyruvate (2-oxopropanoate), 2-oxobutanoate, oxaloacetate (2-oxosuccinate) and 2-oxoglutarate. This diagram illustrates the architecture of chain extension and modification reaction modules for 2-oxocarboxylic acids. The chain extension module RM001 is a tricarboxylic pathway where acetyl-CoA derived carbon is used to extend the chain length by one. The chain modification modules RM002 (including RM032) and RM033, together with a reductive amination step (RC00006 or RC00036), generate basic and branched-chain amino acids, respectively. The modification module RM030 is used in the biosynthesis of glucosinolates, a class of plant secondary metabolites, for conversion to oxime followed by addition of thio-glucose moiety. Furthermore, the chain extension from 2-oxoadipate to 2-oxosuberate is followed by coenzyme B biosynthesis in methonogenic archaea.\nPATHWAY_MAP dme01210  2-Oxocarboxylic acid metabolism\nMODULE      dme_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:dme01210]\n            dme_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:dme01210]\n            dme_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:dme01210]\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nREL_PATHWAY dme00020  Citrate cycle (TCA cycle)\n            dme00220  Arginine biosynthesis\n            dme00250  Alanine, aspartate and glutamate metabolism\n            dme00260  Glycine, serine and threonine metabolism\n            dme00270  Cysteine and methionine metabolism\n            dme00290  Valine, leucine and isoleucine biosynthesis\n            dme00310  Lysine degradation\n            dme00620  Pyruvate metabolism\n            dme00640  Propanoate metabolism\nKO_PATHWAY  ko01210\n///\n\nENTRY       dme01212          Overview  Pathway\nNAME        Fatty acid metabolism - Drosophila melanogaster (fruit fly)\nPATHWAY_MAP dme01212  Fatty acid metabolism\nMODULE      dme_M00082  Fatty acid biosynthesis, initiation [PATH:dme01212]\n            dme_M00083  Fatty acid biosynthesis, elongation [PATH:dme01212]\n            dme_M00085  Fatty acid elongation in mitochondria [PATH:dme01212]\n            dme_M00086  beta-Oxidation, acyl-CoA synthesis [PATH:dme01212]\n            dme_M00087  beta-Oxidation [PATH:dme01212]\n            dme_M00415  Fatty acid elongation in endoplasmic reticulum [PATH:dme01212]\n            dme_M00861  beta-Oxidation, peroxisome, VLCFA [PATH:dme01212]\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nREL_PATHWAY dme00020  Citrate cycle (TCA cycle)\nKO_PATHWAY  ko01212\n///\n\nENTRY       dme01230          Overview  Pathway\nNAME        Biosynthesis of amino acids - Drosophila melanogaster (fruit fly)\nDESCRIPTION This map presents a modular architecture of the biosynthesis pathways of twenty amino acids, which may be viewed as consisting of the core part and its extensions. The core part is the KEGG module for conversion of three-carbon compounds from glyceraldehyde-3P to pyruvate [MD:M00002], together with the pathways around serine and glycine. This KEGG module is the most conserved one in the KEGG MODULE database and is found in almost all the completely sequenced genomes. The extensions are the pathways containing the reaction modules RM001, RM033, RM032, and RM002 for biosynthesis of branched-chain amino acids (left) and basic amino acids (bottom), and the pathways for biosynthesis of histidine and aromatic amino acids (top right). It is interesting to note that the so-called essential amino acids that cannot be synthesized in human and other organisms generally appear in these extensions. Furthermore, the bottom extension of basic amino acids appears to be most divergent containing multiple pathways for lysine biosynthesis and multiple gene sets for arginine biosynthesis.\nPATHWAY_MAP dme01230  Biosynthesis of amino acids\nMODULE      dme_M00002  Glycolysis, core module involving three-carbon compounds [PATH:dme01230]\n            dme_M00005  PRPP biosynthesis, ribose 5P => PRPP [PATH:dme01230]\n            dme_M00007  Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P [PATH:dme01230]\n            dme_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:dme01230]\n            dme_M00015  Proline biosynthesis, glutamate => proline [PATH:dme01230]\n            dme_M00020  Serine biosynthesis, glycerate-3P => serine [PATH:dme01230]\n            dme_M00338  Cysteine biosynthesis, homocysteine + serine => cysteine [PATH:dme01230]\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nKO_PATHWAY  ko01230\n///\n\nENTRY       dme01232          Overview  Pathway\nNAME        Nucleotide metabolism - Drosophila melanogaster (fruit fly)\nPATHWAY_MAP dme01232  Nucleotide metabolism\nMODULE      dme_M00049  Adenine ribonucleotide biosynthesis, IMP => ADP,ATP [PATH:dme01232]\n            dme_M00050  Guanine ribonucleotide biosynthesis, IMP => GDP,GTP [PATH:dme01232]\n            dme_M00052  Pyrimidine ribonucleotide biosynthesis, UMP => UDP/UTP,CDP/CTP [PATH:dme01232]\n            dme_M00053  Deoxyribonucleotide biosynthesis, ADP/GDP/CDP/UDP => dATP/dGTP/dCTP/dUTP [PATH:dme01232]\n            dme_M00938  Pyrimidine deoxyribonucleotide biosynthesis, UDP => dTTP [PATH:dme01232]\n            dme_M00958  Adenine ribonucleotide degradation, AMP => Urate [PATH:dme01232]\n            dme_M00959  Guanine ribonucleotide degradation, GMP => Urate [PATH:dme01232]\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nKO_PATHWAY  ko01232\n///\n\nENTRY       dme01250          Overview  Pathway\nNAME        Biosynthesis of nucleotide sugars - Drosophila melanogaster (fruit fly)\nPATHWAY_MAP dme01250  Biosynthesis of nucleotide sugars\nMODULE      dme_M00549  Nucleotide sugar biosynthesis, glucose => UDP-glucose [PATH:dme01250]\n            dme_M00892  UDP-N-acetyl-D-glucosamine biosynthesis, eukaryotes, glucose => UDP-GlcNAc [PATH:dme01250]\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nKO_PATHWAY  ko01250\n///\n\nENTRY       dme01240          Overview  Pathway\nNAME        Biosynthesis of cofactors - Drosophila melanogaster (fruit fly)\nPATHWAY_MAP dme01240  Biosynthesis of cofactors\nMODULE      dme_M00049  Adenine ribonucleotide biosynthesis, IMP => ADP,ATP [PATH:dme01240]\n            dme_M00051  De novo pyrimidine biosynthesis, glutamine (+ PRPP) => UMP [PATH:dme01240]\n            dme_M00052  Pyrimidine ribonucleotide biosynthesis, UMP => UDP/UTP,CDP/CTP [PATH:dme01240]\n            dme_M00118  Glutathione biosynthesis, glutamate => glutathione [PATH:dme01240]\n            dme_M00120  Coenzyme A biosynthesis, pantothenate => CoA [PATH:dme01240]\n            dme_M00128  Ubiquinone biosynthesis, eukaryotes, 4-hydroxybenzoate + polyprenyl-PP => ubiquinone [PATH:dme01240]\n            dme_M00141  C1-unit interconversion, eukaryotes [PATH:dme01240]\n            dme_M00842  Tetrahydrobiopterin biosynthesis, GTP => BH4 [PATH:dme01240]\n            dme_M00868  Heme biosynthesis, animals and fungi, glycine => heme [PATH:dme01240]\n            dme_M00880  Molybdenum cofactor biosynthesis, GTP => molybdenum cofactor [PATH:dme01240]\n            dme_M00882  Lipoic acid biosynthesis, eukaryotes, octanoyl-ACP => dihydrolipoyl-H [PATH:dme01240]\n            dme_M00883  Lipoic acid biosynthesis, animals and bacteria, octanoyl-ACP => dihydrolipoyl-H => dihydrolipoyl-E2 [PATH:dme01240]\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nKO_PATHWAY  ko01240\n///\n\nENTRY       dme01320          Overview  Pathway\nNAME        Sulfur cycle - Drosophila melanogaster (fruit fly)\nDESCRIPTION Sulfur is one of the six most common chemical elements CHNOPS that constitute living organisms. This map shows a biogeochemical cycle of sulfur compounds and how different microorganisms are responsible for chemical transformations under different environments including atmospheric, hydrospheric and lithospheric environments. Details of chemical reactions and responsible enzymes are shown in map00920 for Sulfur metabolism. Here chemical transformations are represented by KEGG modules, including sulfur reduction [MD:M00986] [KO:K16952] from elemental sulfur to hydrogen sulfide by sulfur-reducing bacteria and archaea, sulfide oxidation [MD:M00985] from hydrogen sulfide to elemental sulfur by sulfur-oxidizing phototrophs, sulfur oxidataion [MD:M00595 M00984] from thiosulfate to sulfate by sulfur-oxidizing chemotrophs, dissimilatory sulfate reduction [MD:M00596] by sulfate-reducing bacteria and archaea, and assimilatory sulfate reduction [MD:M00176 M00987] by both prokaryotes and eukaryotes excluding animals.\nPATHWAY_MAP dme01320  Sulfur cycle\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nKO_PATHWAY  ko01320\n///\n\nENTRY       dme00010                    Pathway\nNAME        Glycolysis / Gluconeogenesis - Drosophila melanogaster (fruit fly)\nDESCRIPTION Glycolysis is the process of converting glucose into pyruvate and generating small amounts of ATP (energy) and NADH (reducing power). It is a central pathway that produces important precursor metabolites: six-carbon compounds of glucose-6P and fructose-6P and three-carbon compounds of glycerone-P, glyceraldehyde-3P, glycerate-3P, phosphoenolpyruvate, and pyruvate [MD:M00001]. Acetyl-CoA, another important precursor metabolite, is produced by oxidative decarboxylation of pyruvate [MD:M00307]. When the enzyme genes of this pathway are examined in completely sequenced genomes, the reaction steps of three-carbon compounds from glycerone-P to pyruvate form a conserved core module [MD:M00002], which is found in almost all organisms and which sometimes contains operon structures in bacterial genomes. Gluconeogenesis is a synthesis pathway of glucose from noncarbohydrate precursors. It is essentially a reversal of glycolysis with minor variations of alternative paths [MD:M00003].\nCLASS       Metabolism; Carbohydrate metabolism\nPATHWAY_MAP dme00010  Glycolysis / Gluconeogenesis\nMODULE      dme_M00001  Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate [PATH:dme00010]\n            dme_M00002  Glycolysis, core module involving three-carbon compounds [PATH:dme00010]\n            dme_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:dme00010]\n            dme_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:dme00010]\nDBLINKS     GO: 0006096 0006094\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nGENE        Dmel_CG10160  Ldh; lactate dehydrogenase, isoform B [KO:K00016] [EC:1.1.1.27]\n            Dmel_CG10202  Pgm2b; phosphoglucomutase 2b [KO:K15779] [EC:5.4.2.2 5.4.2.7]\n            Dmel_CG10467  CG10467; uncharacterized protein [KO:K01785] [EC:5.1.3.3]\n            Dmel_CG10924  Pepck2; phosphoenolpyruvate carboxykinase 2, isoform B [KO:K01596] [EC:4.1.1.32]\n            Dmel_CG10996  CG10996; uncharacterized protein [KO:K01785] [EC:5.1.3.3]\n            Dmel_CG11140  Aldh-III; aldehyde dehydrogenase type III, isoform R [KO:K00129] [EC:1.2.1.5]\n            Dmel_CG11249  CG11249; uncharacterized protein [KO:K00873] [EC:2.7.1.40]\n            Dmel_CG11876  Pdhb; pyruvate dehydrogenase E1 beta subunit, isoform D [KO:K00162] [EC:1.2.4.1]\n            Dmel_CG12055  Gapdh1; glyceraldehyde 3 phosphate dehydrogenase 1, isoform B [KO:K00134] [EC:1.2.1.12]\n            Dmel_CG12229  CG12229; uncharacterized protein [KO:K00873] [EC:2.7.1.40]\n            Dmel_CG13334  CG13334; uncharacterized protein, isoform B [KO:K00016] [EC:1.1.1.27]\n            Dmel_CG15400  G6P; Glucose-6-Phosphatase [KO:K01084] [EC:3.1.3.9]\n            Dmel_CG1721  Pglym78; phosphoglyceromutase 78, isoform C [KO:K01834] [EC:5.4.2.11]\n            Dmel_CG17645  Pglym87; phosphoglyceromutase 87 [KO:K01834] [EC:5.4.2.11]\n            Dmel_CG17654  Eno; enolase, isoform B [KO:K01689] [EC:4.2.1.11]\n            Dmel_CG17725  Pepck1; phosphoenolpyruvate carboxykinase 1 [KO:K01596] [EC:4.1.1.32]\n            Dmel_CG2171  Tpi; triose phosphate isomerase, isoform B [KO:K01803] [EC:5.3.1.1]\n            Dmel_CG2767  CG2767; uncharacterized protein [KO:K00002] [EC:1.1.1.2]\n            Dmel_CG2964  CG2964; uncharacterized protein [KO:K00873] [EC:2.7.1.40]\n            Dmel_CG3001  Hex-A; hexokinase A, isoform C [KO:K00844] [EC:2.7.1.1]\n            Dmel_CG31075  CG31075; uncharacterized protein, isoform B [KO:K00128] [EC:1.2.1.3]\n            Dmel_CG3127  Pgk; phosphoglycerate kinase, isoform B [KO:K00927] [EC:2.7.2.3]\n            Dmel_CG31692  fbp; fructose-1,6-bisphosphatase, isoform C [KO:K03841] [EC:3.1.3.11]\n            Dmel_CG32444  CG32444; uncharacterized protein [KO:K01785] [EC:5.1.3.3]\n            Dmel_CG32445  CG32445; uncharacterized protein [KO:K01785] [EC:5.1.3.3]\n            Dmel_CG32849  Hex-t2; hexokinase testis 2 [KO:K00844] [EC:2.7.1.1]\n            Dmel_CG33102  Hex-t1; hexokinase testis 1 [KO:K00844] [EC:2.7.1.1]\n            Dmel_CG3481  Adh; alcohol dehydrogenase, isoform C [KO:K00001] [EC:1.1.1.1]\n            Dmel_CG3752  Aldh; aldehyde dehydrogenase, isoform B [KO:K00128] [EC:1.2.1.3]\n            Dmel_CG4001  Pfk; phosphofructokinase, isoform B [KO:K00850] [EC:2.7.1.11]\n            Dmel_CG4123  Mipp1; multiple inositol polyphosphate phosphatase 1, isoform C [KO:K03103] [EC:3.1.3.62 3.1.3.80]\n            Dmel_CG4317  Mipp2; multiple inositol polyphosphate phosphatase 2 [KO:K03103] [EC:3.1.3.62 3.1.3.80]\n            Dmel_CG4988  CG4988; uncharacterized protein [KO:K01785] [EC:5.1.3.3]\n            Dmel_CG5165  Pgm1; phosphoglucose mutase 1 [KO:K01835] [EC:5.4.2.2]\n            Dmel_CG5261  muc; midline uncoordinated, isoform C [KO:K00627] [EC:2.3.1.12]\n            Dmel_CG5432  Ald2; aldolase 2, isoform B [KO:K01623] [EC:4.1.2.13]\n            Dmel_CG6058  Ald1; aldolase 1, isoform M [KO:K01623] [EC:4.1.2.13]\n            Dmel_CG6598  Fdh; formaldehyde dehydrogenase [KO:K00121] [EC:1.1.1.284 1.1.1.1]\n            Dmel_CG6650  CG6650; uncharacterized protein, isoform B [KO:K08074] [EC:2.7.1.147]\n            Dmel_CG7010  Pdha; pyruvate dehydrogenase E1 alpha subunit, isoform A [KO:K00161] [EC:1.2.4.1]\n            Dmel_CG7024  CG7024; uncharacterized protein [KO:K00161] [EC:1.2.4.1]\n            Dmel_CG7059  CG7059; uncharacterized protein, isoform A [KO:K01834] [EC:5.4.2.11]\n            Dmel_CG7069  CG7069; uncharacterized protein [KO:K00873] [EC:2.7.1.40]\n            Dmel_CG7070  PyK; pyruvate kinase, isoform A [KO:K00873] [EC:2.7.1.40]\n            Dmel_CG7362  CG7362; uncharacterized protein [KO:K00873] [EC:2.7.1.40]\n            Dmel_CG7430  CG7430; uncharacterized protein, isoform B [KO:K00382] [EC:1.8.1.4]\n            Dmel_CG8073  Pgm2a; phosphoglucomutase 2a [KO:K01835] [EC:5.4.2.2]\n            Dmel_CG8094  Hex-C; hexokinase C [KO:K00844] [EC:2.7.1.1]\n            Dmel_CG8251  Pgi; phosphoglucose isomerase, isoform A [KO:K01810] [EC:5.3.1.9]\n            Dmel_CG8893  Gapdh2; glyceraldehyde 3 phosphate dehydrogenase 2, isoform C [KO:K00134] [EC:1.2.1.12]\n            Dmel_CG9008  CG9008; uncharacterized protein, isoform D [KO:K01792] [EC:5.1.3.15]\n            Dmel_CG9010  CG9010; uncharacterized protein [KO:K00134] [EC:1.2.1.12]\n            Dmel_CG9390  AcCoAS; acetyl coenzyme A synthase, isoform D [KO:K01895] [EC:6.2.1.1]\n            Dmel_CG9629  Aldh7A1; aldehyde dehydrogenase 7 family member A1 [KO:K14085] [EC:1.2.1.31 1.2.1.8 1.2.1.3]\n            Dmel_CG9961  CG9961; uncharacterized protein, isoform B [KO:K00927] [EC:2.7.2.3]\nCOMPOUND    C00022  Pyruvate\n            C00024  Acetyl-CoA\n            C00031  D-Glucose\n            C00033  Acetate\n            C00036  Oxaloacetate\n            C00068  Thiamin diphosphate\n            C00074  Phosphoenolpyruvate\n            C00084  Acetaldehyde\n            C00085  D-Fructose 6-phosphate\n            C00103  D-Glucose 1-phosphate\n            C00111  Glycerone phosphate\n            C00118  D-Glyceraldehyde 3-phosphate\n            C00186  (S)-Lactate\n            C00197  3-Phospho-D-glycerate\n            C00221  beta-D-Glucose\n            C00236  3-Phospho-D-glyceroyl phosphate\n            C00267  alpha-D-Glucose\n            C00354  D-Fructose 1,6-bisphosphate\n            C00469  Ethanol\n            C00631  2-Phospho-D-glycerate\n            C00668  alpha-D-Glucose 6-phosphate\n            C01159  2,3-Bisphospho-D-glycerate\n            C01172  beta-D-Glucose 6-phosphate\n            C01451  Salicin\n            C05125  2-(alpha-Hydroxyethyl)thiamine diphosphate\n            C06186  Arbutin\n            C06187  Arbutin 6-phosphate\n            C06188  Salicin 6-phosphate\n            C15972  Enzyme N6-(lipoyl)lysine\n            C15973  Enzyme N6-(dihydrolipoyl)lysine\n            C16255  [Dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine\nREFERENCE   \n  AUTHORS   Nishizuka Y (ed).\n  TITLE     [Metabolic Maps] (In Japanese)\n  JOURNAL   Tokyo Kagaku Dojin (1980)\nREFERENCE   \n  AUTHORS   Nishizuka Y, Seyama Y, Ikai A, Ishimura Y, Kawaguchi A (eds).\n  TITLE     [Cellular Functions and Metabolic Maps] (In Japanese)\n  JOURNAL   Tokyo Kagaku Dojin (1997)\nREFERENCE   \n  AUTHORS   Michal G.\n  TITLE     Biochemical Pathways\n  JOURNAL   Wiley (1999)\nREL_PATHWAY dme00020  Citrate cycle (TCA cycle)\n            dme00030  Pentose phosphate pathway\n            dme00500  Starch and sucrose metabolism\n            dme00620  Pyruvate metabolism\n            dme00640  Propanoate metabolism\nKO_PATHWAY  ko00010\n///")
   8.             └─ffrec$setBody(value)
  
  [ FAIL 1 | WARN 6 | SKIP 0 | PASS 562 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/BiocSet.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocSet
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘BiocSet’ ...
** this is package ‘BiocSet’ version ‘1.21.0’
** 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 (BiocSet)

R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(BiocSet)
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 
> test_check("BiocSet")
[ FAIL 1 | WARN 6 | SKIP 0 | PASS 562 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_mapping_set.R:63:5'): 'kegg_sets()' works ──────────────────────
Error in `if (.self$lastField == "REFERENCE") {
    if (length(.self$lastSubfield)) {
        if (is.null(.self$lastReference[[.self$lastSubfield]])) 
            .self$lastReference[[.self$lastSubfield]] <- c()
        .self$lastReference[[.self$lastSubfield]] <- c(.self$lastReference[[.self$lastSubfield]], 
            body)
    }
    else {
        if (is.null(.self$lastReference[[.self$lastField]])) 
            .self$lastReference[[.self$lastField]] <- c()
        .self$lastReference[[.self$lastField]] <- c(.self$lastReference[[.self$lastField]], 
            body)
    }
} else {
    if (is.null(.self$fields[[.self$lastField]])) 
        .self$fields[[.self$lastField]] <- list()
    if (length(.self$lastSubfield)) {
        if (is.null(.self$fields[[.self$lastField]][[.self$lastSubfield]])) 
            .self$fields[[.self$lastField]][[.self$lastSubfield]] <- c()
        .self$fields[[.self$lastField]][[.self$lastSubfield]] <- c(.self$fields[[.self$lastField]][[.self$lastSubfield]], 
            body)
    }
    else {
        if (is.null(.self$fields[[.self$lastField]][[.self$lastField]])) 
            .self$fields[[.self$lastField]][[.self$lastField]] <- c()
        .self$fields[[.self$lastField]][[.self$lastField]] <- c(.self$fields[[.self$lastField]][[.self$lastField]], 
            body)
    }
}`: missing value where TRUE/FALSE needed
Backtrace:
    ▆
 1. └─BiocSet::kegg_sets("dme") at test_mapping_set.R:63:5
 2.   └─base::lapply(...)
 3.     └─BiocSet (local) FUN(X[[i]], ...)
 4.       └─KEGGREST::keggGet(x)
 5.         └─KEGGREST:::.getUrl(url, .flatFileParser)
 6.           ├─base::do.call(parser, list(content, ...))
 7.           └─KEGGREST (local) `<fn>`("ENTRY       dme01100          Global    Pathway\nNAME        Metabolic pathways - Drosophila melanogaster (fruit fly)\nPATHWAY_MAP dme01100  Metabolic pathways\nMODULE      dme_M00001  Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate [PATH:dme01100]\n            dme_M00002  Glycolysis, core module involving three-carbon compounds [PATH:dme01100]\n            dme_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:dme01100]\n            dme_M00004  Pentose phosphate pathway (Pentose phosphate cycle) [PATH:dme01100]\n            dme_M00005  PRPP biosynthesis, ribose 5P => PRPP [PATH:dme01100]\n            dme_M00006  Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P [PATH:dme01100]\n            dme_M00007  Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P [PATH:dme01100]\n            dme_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:dme01100]\n            dme_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:dme01100]\n            dme_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:dme01100]\n            dme_M00013  Malonate semialdehyde pathway, propanoyl-CoA => acetyl-CoA [PATH:dme01100]\n            dme_M00014  Glucuronate pathway (uronate pathway) [PATH:dme01100]\n            dme_M00015  Proline biosynthesis, glutamate => proline [PATH:dme01100]\n            dme_M00020  Serine biosynthesis, glycerate-3P => serine [PATH:dme01100]\n            dme_M00027  GABA (gamma-Aminobutyrate) shunt [PATH:dme01100]\n            dme_M00034  Methionine salvage pathway [PATH:dme01100]\n            dme_M00035  Methionine degradation [PATH:dme01100]\n            dme_M00036  Leucine degradation, leucine => acetoacetate + acetyl-CoA [PATH:dme01100]\n            dme_M00044  Tyrosine degradation, tyrosine => homogentisate [PATH:dme01100]\n            dme_M00046  Pyrimidine degradation, uracil => beta-alanine, thymine => 3-aminoisobutanoate [PATH:dme01100]\n            dme_M00048  De novo purine biosynthesis, PRPP + glutamine => IMP [PATH:dme01100]\n            dme_M00049  Adenine ribonucleotide biosynthesis, IMP => ADP,ATP [PATH:dme01100]\n            dme_M00050  Guanine ribonucleotide biosynthesis, IMP => GDP,GTP [PATH:dme01100]\n            dme_M00051  De novo pyrimidine biosynthesis, glutamine (+ PRPP) => UMP [PATH:dme01100]\n            dme_M00052  Pyrimidine ribonucleotide biosynthesis, UMP => UDP/UTP,CDP/CTP [PATH:dme01100]\n            dme_M00053  Deoxyribonucleotide biosynthesis, ADP/GDP/CDP/UDP => dATP/dGTP/dCTP/dUTP [PATH:dme01100]\n            dme_M00057  Glycosaminoglycan biosynthesis, linkage tetrasaccharide [PATH:dme01100]\n            dme_M00058  Glycosaminoglycan biosynthesis, chondroitin sulfate backbone [PATH:dme01100]\n            dme_M00059  Glycosaminoglycan biosynthesis, heparan sulfate backbone [PATH:dme01100]\n            dme_M00073  N-glycan precursor trimming [PATH:dme01100]\n            dme_M00082  Fatty acid biosynthesis, initiation [PATH:dme01100]\n            dme_M00083  Fatty acid biosynthesis, elongation [PATH:dme01100]\n            dme_M00085  Fatty acid elongation in mitochondria [PATH:dme01100]\n            dme_M00086  beta-Oxidation, acyl-CoA synthesis [PATH:dme01100]\n            dme_M00087  beta-Oxidation [PATH:dme01100]\n            dme_M00089  Triacylglycerol biosynthesis [PATH:dme01100]\n            dme_M00092  Phosphatidylethanolamine (PE) biosynthesis, ethanolamine => PE [PATH:dme01100]\n            dme_M00094  Ceramide biosynthesis [PATH:dme01100]\n            dme_M00095  C5 isoprenoid biosynthesis, mevalonate pathway [PATH:dme01100]\n            dme_M00099  Sphingosine biosynthesis [PATH:dme01100]\n            dme_M00100  Sphingosine degradation [PATH:dme01100]\n            dme_M00118  Glutathione biosynthesis, glutamate => glutathione [PATH:dme01100]\n            dme_M00120  Coenzyme A biosynthesis, pantothenate => CoA [PATH:dme01100]\n            dme_M00128  Ubiquinone biosynthesis, eukaryotes, 4-hydroxybenzoate + polyprenyl-PP => ubiquinone [PATH:dme01100]\n            dme_M00130  Inositol phosphate metabolism, PI=> PIP2 => Ins(1,4,5)P3 => Ins(1,3,4,5)P4 [PATH:dme01100]\n            dme_M00131  Inositol phosphate metabolism, Ins(1,3,4,5)P4 => Ins(1,3,4)P3 => myo-inositol [PATH:dme01100]\n            dme_M00134  Polyamine biosynthesis, arginine => ornithine => putrescine [PATH:dme01100]\n            dme_M00141  C1-unit interconversion, eukaryotes [PATH:dme01100]\n            dme_M00142  NADH:ubiquinone oxidoreductase, mitochondria [PATH:dme01100]\n            dme_M00143  NADH dehydrogenase (ubiquinone) Fe-S protein/flavoprotein complex, mitochondria [PATH:dme01100]\n            dme_M00148  Succinate dehydrogenase (ubiquinone) [PATH:dme01100]\n            dme_M00151  Cytochrome bc1 complex respiratory unit [PATH:dme01100]\n            dme_M00154  Cytochrome c oxidase [PATH:dme01100]\n            dme_M00158  F-type ATPase, eukaryotes [PATH:dme01100]\n            dme_M00160  V-type ATPase, eukaryotes [PATH:dme01100]\n            dme_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:dme01100]\n            dme_M00338  Cysteine biosynthesis, homocysteine + serine => cysteine [PATH:dme01100]\n            dme_M00367  C10-C20 isoprenoid biosynthesis, non-plant eukaryotes [PATH:dme01100]\n            dme_M00415  Fatty acid elongation in endoplasmic reticulum [PATH:dme01100]\n            dme_M00549  Nucleotide sugar biosynthesis, glucose => UDP-glucose [PATH:dme01100]\n            dme_M00621  Glycine cleavage system [PATH:dme01100]\n            dme_M00842  Tetrahydrobiopterin biosynthesis, GTP => BH4 [PATH:dme01100]\n            dme_M00854  Glycogen biosynthesis, glucose-1P => glycogen/starch [PATH:dme01100]\n            dme_M00855  Glycogen degradation, glycogen => glucose-6P [PATH:dme01100]\n            dme_M00861  beta-Oxidation, peroxisome, VLCFA [PATH:dme01100]\n            dme_M00868  Heme biosynthesis, animals and fungi, glycine => heme [PATH:dme01100]\n            dme_M00880  Molybdenum cofactor biosynthesis, GTP => molybdenum cofactor [PATH:dme01100]\n            dme_M00882  Lipoic acid biosynthesis, eukaryotes, octanoyl-ACP => dihydrolipoyl-H [PATH:dme01100]\n            dme_M00883  Lipoic acid biosynthesis, animals and bacteria, octanoyl-ACP => dihydrolipoyl-H => dihydrolipoyl-E2 [PATH:dme01100]\n            dme_M00892  UDP-N-acetyl-D-glucosamine biosynthesis, eukaryotes, glucose => UDP-GlcNAc [PATH:dme01100]\n            dme_M00938  Pyrimidine deoxyribonucleotide biosynthesis, UDP => dTTP [PATH:dme01100]\n            dme_M00958  Adenine ribonucleotide degradation, AMP => Urate [PATH:dme01100]\n            dme_M00959  Guanine ribonucleotide degradation, GMP => Urate [PATH:dme01100]\n            dme_M00970  Proline degradation, proline => glutamate [PATH:dme01100]\n            dme_M00972  Proline metabolism [PATH:dme01100]\n            dme_M00983  GPI-anchor remodeling [PATH:dme01100]\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nREL_PATHWAY dme00010  Glycolysis / Gluconeogenesis\n            dme00020  Citrate cycle (TCA cycle)\n            dme00030  Pentose phosphate pathway\n            dme00040  Pentose and glucuronate interconversions\n            dme00051  Fructose and mannose metabolism\n            dme00052  Galactose metabolism\n            dme00053  Ascorbate and aldarate metabolism\n            dme00061  Fatty acid biosynthesis\n            dme00062  Fatty acid elongation\n            dme00071  Fatty acid degradation\n            dme00100  Steroid biosynthesis\n            dme00130  Ubiquinone and other terpenoid-quinone biosynthesis\n            dme00190  Oxidative phosphorylation\n            dme00220  Arginine biosynthesis\n            dme00230  Purine metabolism\n            dme00232  Caffeine metabolism\n            dme00240  Pyrimidine metabolism\n            dme00250  Alanine, aspartate and glutamate metabolism\n            dme00260  Glycine, serine and threonine metabolism\n            dme00270  Cysteine and methionine metabolism\n            dme00280  Valine, leucine and isoleucine degradation\n            dme00290  Valine, leucine and isoleucine biosynthesis\n            dme00310  Lysine degradation\n            dme00330  Arginine and proline metabolism\n            dme00340  Histidine metabolism\n            dme00350  Tyrosine metabolism\n            dme00360  Phenylalanine metabolism\n            dme00380  Tryptophan metabolism\n            dme00400  Phenylalanine, tyrosine and tryptophan biosynthesis\n            dme00410  beta-Alanine metabolism\n            dme00430  Taurine and hypotaurine metabolism\n            dme00440  Phosphonate and phosphinate metabolism\n            dme00450  Selenocompound metabolism\n            dme00470  D-Amino acid metabolism\n            dme00480  Glutathione metabolism\n            dme00500  Starch and sucrose metabolism\n            dme00510  N-Glycan biosynthesis\n            dme00511  Other glycan degradation\n            dme00512  Mucin type O-glycan biosynthesis\n            dme00513  Various types of N-glycan biosynthesis\n            dme00514  Other types of O-glycan biosynthesis\n            dme00515  Mannose type O-glycan biosynthesis\n            dme00520  Amino sugar and nucleotide sugar metabolism\n            dme00531  Glycosaminoglycan degradation\n            dme00532  Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate\n            dme00534  Glycosaminoglycan biosynthesis - heparan sulfate / heparin\n            dme00541  Biosynthesis of various nucleotide sugars\n            dme00561  Glycerolipid metabolism\n            dme00562  Inositol phosphate metabolism\n            dme00563  Glycosylphosphatidylinositol (GPI)-anchor biosynthesis\n            dme00564  Glycerophospholipid metabolism\n            dme00565  Ether lipid metabolism\n            dme00590  Arachidonic acid metabolism\n            dme00592  alpha-Linolenic acid metabolism\n            dme00600  Sphingolipid metabolism\n            dme00601  Glycosphingolipid biosynthesis - lacto and neolacto series\n            dme00603  Glycosphingolipid biosynthesis - globo and isoglobo series\n            dme00604  Glycosphingolipid biosynthesis - ganglio series\n            dme00620  Pyruvate metabolism\n            dme00630  Glyoxylate and dicarboxylate metabolism\n            dme00640  Propanoate metabolism\n            dme00650  Butanoate metabolism\n            dme00670  One carbon pool by folate\n            dme00730  Thiamine metabolism\n            dme00740  Riboflavin metabolism\n            dme00750  Vitamin B6 metabolism\n            dme00760  Nicotinate and nicotinamide metabolism\n            dme00770  Pantothenate and CoA biosynthesis\n            dme00780  Biotin metabolism\n            dme00785  Lipoic acid metabolism\n            dme00790  Folate biosynthesis\n            dme00830  Retinol metabolism\n            dme00860  Porphyrin metabolism\n            dme00900  Terpenoid backbone biosynthesis\n            dme00910  Nitrogen metabolism\n            dme00920  Sulfur metabolism\n            dme00980  Metabolism of xenobiotics by cytochrome P450\n            dme00981  Insect hormone biosynthesis\n            dme00982  Drug metabolism - cytochrome P450\n            dme00983  Drug metabolism - other enzymes\n            dme01040  Biosynthesis of unsaturated fatty acids\nKO_PATHWAY  ko01100\n///\n\nENTRY       dme01200          Overview  Pathway\nNAME        Carbon metabolism - Drosophila melanogaster (fruit fly)\nDESCRIPTION Carbon metabolism is the most basic aspect of life. This map presents an overall view of central carbon metabolism, where the number of carbons is shown for each compound denoted by a circle, excluding a cofactor (CoA, CoM, THF, or THMPT) that is replaced by an asterisk. The map contains carbon utilization pathways of glycolysis (map00010), pentose phosphate pathway (map00030), and citrate cycle (map00020), and six known carbon fixation pathways (map00710 and map00720) as well as some pathways of methane metabolism (map00680). The six carbon fixation pathways are: (1) reductive pentose phosphate cycle (Calvin cycle) in plants and cyanobacteria that perform oxygenic photosynthesis, (2) reductive citrate cycle in photosynthetic green sulfur bacteria and some chemolithoautotrophs, (3) 3-hydroxypropionate bi-cycle in photosynthetic green nonsulfur bacteria, two variants of 4-hydroxybutyrate pathways in Crenarchaeota called (4) hydroxypropionate-hydroxybutyrate cycle and (5) dicarboxylate-hydroxybutyrate cycle, and (6) reductive acetyl-CoA pathway in methanogenic bacteria.\nPATHWAY_MAP dme01200  Carbon metabolism\nMODULE      dme_M00001  Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate [PATH:dme01200]\n            dme_M00002  Glycolysis, core module involving three-carbon compounds [PATH:dme01200]\n            dme_M00004  Pentose phosphate pathway (Pentose phosphate cycle) [PATH:dme01200]\n            dme_M00005  PRPP biosynthesis, ribose 5P => PRPP [PATH:dme01200]\n            dme_M00006  Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P [PATH:dme01200]\n            dme_M00007  Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P [PATH:dme01200]\n            dme_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:dme01200]\n            dme_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:dme01200]\n            dme_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:dme01200]\n            dme_M00013  Malonate semialdehyde pathway, propanoyl-CoA => acetyl-CoA [PATH:dme01200]\n            dme_M00020  Serine biosynthesis, glycerate-3P => serine [PATH:dme01200]\n            dme_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:dme01200]\n            dme_M00621  Glycine cleavage system [PATH:dme01200]\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nKO_PATHWAY  ko01200\n///\n\nENTRY       dme01210          Overview  Pathway\nNAME        2-Oxocarboxylic acid metabolism - Drosophila melanogaster (fruit fly)\nDESCRIPTION 2-Oxocarboxylic acids, also called 2-oxo acids and alpha-keto acids, are the most elementary set of metabolites that includes pyruvate (2-oxopropanoate), 2-oxobutanoate, oxaloacetate (2-oxosuccinate) and 2-oxoglutarate. This diagram illustrates the architecture of chain extension and modification reaction modules for 2-oxocarboxylic acids. The chain extension module RM001 is a tricarboxylic pathway where acetyl-CoA derived carbon is used to extend the chain length by one. The chain modification modules RM002 (including RM032) and RM033, together with a reductive amination step (RC00006 or RC00036), generate basic and branched-chain amino acids, respectively. The modification module RM030 is used in the biosynthesis of glucosinolates, a class of plant secondary metabolites, for conversion to oxime followed by addition of thio-glucose moiety. Furthermore, the chain extension from 2-oxoadipate to 2-oxosuberate is followed by coenzyme B biosynthesis in methonogenic archaea.\nPATHWAY_MAP dme01210  2-Oxocarboxylic acid metabolism\nMODULE      dme_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:dme01210]\n            dme_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:dme01210]\n            dme_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:dme01210]\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nREL_PATHWAY dme00020  Citrate cycle (TCA cycle)\n            dme00220  Arginine biosynthesis\n            dme00250  Alanine, aspartate and glutamate metabolism\n            dme00260  Glycine, serine and threonine metabolism\n            dme00270  Cysteine and methionine metabolism\n            dme00290  Valine, leucine and isoleucine biosynthesis\n            dme00310  Lysine degradation\n            dme00620  Pyruvate metabolism\n            dme00640  Propanoate metabolism\nKO_PATHWAY  ko01210\n///\n\nENTRY       dme01212          Overview  Pathway\nNAME        Fatty acid metabolism - Drosophila melanogaster (fruit fly)\nPATHWAY_MAP dme01212  Fatty acid metabolism\nMODULE      dme_M00082  Fatty acid biosynthesis, initiation [PATH:dme01212]\n            dme_M00083  Fatty acid biosynthesis, elongation [PATH:dme01212]\n            dme_M00085  Fatty acid elongation in mitochondria [PATH:dme01212]\n            dme_M00086  beta-Oxidation, acyl-CoA synthesis [PATH:dme01212]\n            dme_M00087  beta-Oxidation [PATH:dme01212]\n            dme_M00415  Fatty acid elongation in endoplasmic reticulum [PATH:dme01212]\n            dme_M00861  beta-Oxidation, peroxisome, VLCFA [PATH:dme01212]\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nREL_PATHWAY dme00020  Citrate cycle (TCA cycle)\nKO_PATHWAY  ko01212\n///\n\nENTRY       dme01230          Overview  Pathway\nNAME        Biosynthesis of amino acids - Drosophila melanogaster (fruit fly)\nDESCRIPTION This map presents a modular architecture of the biosynthesis pathways of twenty amino acids, which may be viewed as consisting of the core part and its extensions. The core part is the KEGG module for conversion of three-carbon compounds from glyceraldehyde-3P to pyruvate [MD:M00002], together with the pathways around serine and glycine. This KEGG module is the most conserved one in the KEGG MODULE database and is found in almost all the completely sequenced genomes. The extensions are the pathways containing the reaction modules RM001, RM033, RM032, and RM002 for biosynthesis of branched-chain amino acids (left) and basic amino acids (bottom), and the pathways for biosynthesis of histidine and aromatic amino acids (top right). It is interesting to note that the so-called essential amino acids that cannot be synthesized in human and other organisms generally appear in these extensions. Furthermore, the bottom extension of basic amino acids appears to be most divergent containing multiple pathways for lysine biosynthesis and multiple gene sets for arginine biosynthesis.\nPATHWAY_MAP dme01230  Biosynthesis of amino acids\nMODULE      dme_M00002  Glycolysis, core module involving three-carbon compounds [PATH:dme01230]\n            dme_M00005  PRPP biosynthesis, ribose 5P => PRPP [PATH:dme01230]\n            dme_M00007  Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P [PATH:dme01230]\n            dme_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:dme01230]\n            dme_M00015  Proline biosynthesis, glutamate => proline [PATH:dme01230]\n            dme_M00020  Serine biosynthesis, glycerate-3P => serine [PATH:dme01230]\n            dme_M00338  Cysteine biosynthesis, homocysteine + serine => cysteine [PATH:dme01230]\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nKO_PATHWAY  ko01230\n///\n\nENTRY       dme01232          Overview  Pathway\nNAME        Nucleotide metabolism - Drosophila melanogaster (fruit fly)\nPATHWAY_MAP dme01232  Nucleotide metabolism\nMODULE      dme_M00049  Adenine ribonucleotide biosynthesis, IMP => ADP,ATP [PATH:dme01232]\n            dme_M00050  Guanine ribonucleotide biosynthesis, IMP => GDP,GTP [PATH:dme01232]\n            dme_M00052  Pyrimidine ribonucleotide biosynthesis, UMP => UDP/UTP,CDP/CTP [PATH:dme01232]\n            dme_M00053  Deoxyribonucleotide biosynthesis, ADP/GDP/CDP/UDP => dATP/dGTP/dCTP/dUTP [PATH:dme01232]\n            dme_M00938  Pyrimidine deoxyribonucleotide biosynthesis, UDP => dTTP [PATH:dme01232]\n            dme_M00958  Adenine ribonucleotide degradation, AMP => Urate [PATH:dme01232]\n            dme_M00959  Guanine ribonucleotide degradation, GMP => Urate [PATH:dme01232]\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nKO_PATHWAY  ko01232\n///\n\nENTRY       dme01250          Overview  Pathway\nNAME        Biosynthesis of nucleotide sugars - Drosophila melanogaster (fruit fly)\nPATHWAY_MAP dme01250  Biosynthesis of nucleotide sugars\nMODULE      dme_M00549  Nucleotide sugar biosynthesis, glucose => UDP-glucose [PATH:dme01250]\n            dme_M00892  UDP-N-acetyl-D-glucosamine biosynthesis, eukaryotes, glucose => UDP-GlcNAc [PATH:dme01250]\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nKO_PATHWAY  ko01250\n///\n\nENTRY       dme01240          Overview  Pathway\nNAME        Biosynthesis of cofactors - Drosophila melanogaster (fruit fly)\nPATHWAY_MAP dme01240  Biosynthesis of cofactors\nMODULE      dme_M00049  Adenine ribonucleotide biosynthesis, IMP => ADP,ATP [PATH:dme01240]\n            dme_M00051  De novo pyrimidine biosynthesis, glutamine (+ PRPP) => UMP [PATH:dme01240]\n            dme_M00052  Pyrimidine ribonucleotide biosynthesis, UMP => UDP/UTP,CDP/CTP [PATH:dme01240]\n            dme_M00118  Glutathione biosynthesis, glutamate => glutathione [PATH:dme01240]\n            dme_M00120  Coenzyme A biosynthesis, pantothenate => CoA [PATH:dme01240]\n            dme_M00128  Ubiquinone biosynthesis, eukaryotes, 4-hydroxybenzoate + polyprenyl-PP => ubiquinone [PATH:dme01240]\n            dme_M00141  C1-unit interconversion, eukaryotes [PATH:dme01240]\n            dme_M00842  Tetrahydrobiopterin biosynthesis, GTP => BH4 [PATH:dme01240]\n            dme_M00868  Heme biosynthesis, animals and fungi, glycine => heme [PATH:dme01240]\n            dme_M00880  Molybdenum cofactor biosynthesis, GTP => molybdenum cofactor [PATH:dme01240]\n            dme_M00882  Lipoic acid biosynthesis, eukaryotes, octanoyl-ACP => dihydrolipoyl-H [PATH:dme01240]\n            dme_M00883  Lipoic acid biosynthesis, animals and bacteria, octanoyl-ACP => dihydrolipoyl-H => dihydrolipoyl-E2 [PATH:dme01240]\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nKO_PATHWAY  ko01240\n///\n\nENTRY       dme01320          Overview  Pathway\nNAME        Sulfur cycle - Drosophila melanogaster (fruit fly)\nDESCRIPTION Sulfur is one of the six most common chemical elements CHNOPS that constitute living organisms. This map shows a biogeochemical cycle of sulfur compounds and how different microorganisms are responsible for chemical transformations under different environments including atmospheric, hydrospheric and lithospheric environments. Details of chemical reactions and responsible enzymes are shown in map00920 for Sulfur metabolism. Here chemical transformations are represented by KEGG modules, including sulfur reduction [MD:M00986] [KO:K16952] from elemental sulfur to hydrogen sulfide by sulfur-reducing bacteria and archaea, sulfide oxidation [MD:M00985] from hydrogen sulfide to elemental sulfur by sulfur-oxidizing phototrophs, sulfur oxidataion [MD:M00595 M00984] from thiosulfate to sulfate by sulfur-oxidizing chemotrophs, dissimilatory sulfate reduction [MD:M00596] by sulfate-reducing bacteria and archaea, and assimilatory sulfate reduction [MD:M00176 M00987] by both prokaryotes and eukaryotes excluding animals.\nPATHWAY_MAP dme01320  Sulfur cycle\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nKO_PATHWAY  ko01320\n///\n\nENTRY       dme00010                    Pathway\nNAME        Glycolysis / Gluconeogenesis - Drosophila melanogaster (fruit fly)\nDESCRIPTION Glycolysis is the process of converting glucose into pyruvate and generating small amounts of ATP (energy) and NADH (reducing power). It is a central pathway that produces important precursor metabolites: six-carbon compounds of glucose-6P and fructose-6P and three-carbon compounds of glycerone-P, glyceraldehyde-3P, glycerate-3P, phosphoenolpyruvate, and pyruvate [MD:M00001]. Acetyl-CoA, another important precursor metabolite, is produced by oxidative decarboxylation of pyruvate [MD:M00307]. When the enzyme genes of this pathway are examined in completely sequenced genomes, the reaction steps of three-carbon compounds from glycerone-P to pyruvate form a conserved core module [MD:M00002], which is found in almost all organisms and which sometimes contains operon structures in bacterial genomes. Gluconeogenesis is a synthesis pathway of glucose from noncarbohydrate precursors. It is essentially a reversal of glycolysis with minor variations of alternative paths [MD:M00003].\nCLASS       Metabolism; Carbohydrate metabolism\nPATHWAY_MAP dme00010  Glycolysis / Gluconeogenesis\nMODULE      dme_M00001  Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate [PATH:dme00010]\n            dme_M00002  Glycolysis, core module involving three-carbon compounds [PATH:dme00010]\n            dme_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:dme00010]\n            dme_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:dme00010]\nDBLINKS     GO: 0006096 0006094\nORGANISM    Drosophila melanogaster (fruit fly) [GN:dme]\nGENE        Dmel_CG10160  Ldh; lactate dehydrogenase, isoform B [KO:K00016] [EC:1.1.1.27]\n            Dmel_CG10202  Pgm2b; phosphoglucomutase 2b [KO:K15779] [EC:5.4.2.2 5.4.2.7]\n            Dmel_CG10467  CG10467; uncharacterized protein [KO:K01785] [EC:5.1.3.3]\n            Dmel_CG10924  Pepck2; phosphoenolpyruvate carboxykinase 2, isoform B [KO:K01596] [EC:4.1.1.32]\n            Dmel_CG10996  CG10996; uncharacterized protein [KO:K01785] [EC:5.1.3.3]\n            Dmel_CG11140  Aldh-III; aldehyde dehydrogenase type III, isoform R [KO:K00129] [EC:1.2.1.5]\n            Dmel_CG11249  CG11249; uncharacterized protein [KO:K00873] [EC:2.7.1.40]\n            Dmel_CG11876  Pdhb; pyruvate dehydrogenase E1 beta subunit, isoform D [KO:K00162] [EC:1.2.4.1]\n            Dmel_CG12055  Gapdh1; glyceraldehyde 3 phosphate dehydrogenase 1, isoform B [KO:K00134] [EC:1.2.1.12]\n            Dmel_CG12229  CG12229; uncharacterized protein [KO:K00873] [EC:2.7.1.40]\n            Dmel_CG13334  CG13334; uncharacterized protein, isoform B [KO:K00016] [EC:1.1.1.27]\n            Dmel_CG15400  G6P; Glucose-6-Phosphatase [KO:K01084] [EC:3.1.3.9]\n            Dmel_CG1721  Pglym78; phosphoglyceromutase 78, isoform C [KO:K01834] [EC:5.4.2.11]\n            Dmel_CG17645  Pglym87; phosphoglyceromutase 87 [KO:K01834] [EC:5.4.2.11]\n            Dmel_CG17654  Eno; enolase, isoform B [KO:K01689] [EC:4.2.1.11]\n            Dmel_CG17725  Pepck1; phosphoenolpyruvate carboxykinase 1 [KO:K01596] [EC:4.1.1.32]\n            Dmel_CG2171  Tpi; triose phosphate isomerase, isoform B [KO:K01803] [EC:5.3.1.1]\n            Dmel_CG2767  CG2767; uncharacterized protein [KO:K00002] [EC:1.1.1.2]\n            Dmel_CG2964  CG2964; uncharacterized protein [KO:K00873] [EC:2.7.1.40]\n            Dmel_CG3001  Hex-A; hexokinase A, isoform C [KO:K00844] [EC:2.7.1.1]\n            Dmel_CG31075  CG31075; uncharacterized protein, isoform B [KO:K00128] [EC:1.2.1.3]\n            Dmel_CG3127  Pgk; phosphoglycerate kinase, isoform B [KO:K00927] [EC:2.7.2.3]\n            Dmel_CG31692  fbp; fructose-1,6-bisphosphatase, isoform C [KO:K03841] [EC:3.1.3.11]\n            Dmel_CG32444  CG32444; uncharacterized protein [KO:K01785] [EC:5.1.3.3]\n            Dmel_CG32445  CG32445; uncharacterized protein [KO:K01785] [EC:5.1.3.3]\n            Dmel_CG32849  Hex-t2; hexokinase testis 2 [KO:K00844] [EC:2.7.1.1]\n            Dmel_CG33102  Hex-t1; hexokinase testis 1 [KO:K00844] [EC:2.7.1.1]\n            Dmel_CG3481  Adh; alcohol dehydrogenase, isoform C [KO:K00001] [EC:1.1.1.1]\n            Dmel_CG3752  Aldh; aldehyde dehydrogenase, isoform B [KO:K00128] [EC:1.2.1.3]\n            Dmel_CG4001  Pfk; phosphofructokinase, isoform B [KO:K00850] [EC:2.7.1.11]\n            Dmel_CG4123  Mipp1; multiple inositol polyphosphate phosphatase 1, isoform C [KO:K03103] [EC:3.1.3.62 3.1.3.80]\n            Dmel_CG4317  Mipp2; multiple inositol polyphosphate phosphatase 2 [KO:K03103] [EC:3.1.3.62 3.1.3.80]\n            Dmel_CG4988  CG4988; uncharacterized protein [KO:K01785] [EC:5.1.3.3]\n            Dmel_CG5165  Pgm1; phosphoglucose mutase 1 [KO:K01835] [EC:5.4.2.2]\n            Dmel_CG5261  muc; midline uncoordinated, isoform C [KO:K00627] [EC:2.3.1.12]\n            Dmel_CG5432  Ald2; aldolase 2, isoform B [KO:K01623] [EC:4.1.2.13]\n            Dmel_CG6058  Ald1; aldolase 1, isoform M [KO:K01623] [EC:4.1.2.13]\n            Dmel_CG6598  Fdh; formaldehyde dehydrogenase [KO:K00121] [EC:1.1.1.284 1.1.1.1]\n            Dmel_CG6650  CG6650; uncharacterized protein, isoform B [KO:K08074] [EC:2.7.1.147]\n            Dmel_CG7010  Pdha; pyruvate dehydrogenase E1 alpha subunit, isoform A [KO:K00161] [EC:1.2.4.1]\n            Dmel_CG7024  CG7024; uncharacterized protein [KO:K00161] [EC:1.2.4.1]\n            Dmel_CG7059  CG7059; uncharacterized protein, isoform A [KO:K01834] [EC:5.4.2.11]\n            Dmel_CG7069  CG7069; uncharacterized protein [KO:K00873] [EC:2.7.1.40]\n            Dmel_CG7070  PyK; pyruvate kinase, isoform A [KO:K00873] [EC:2.7.1.40]\n            Dmel_CG7362  CG7362; uncharacterized protein [KO:K00873] [EC:2.7.1.40]\n            Dmel_CG7430  CG7430; uncharacterized protein, isoform B [KO:K00382] [EC:1.8.1.4]\n            Dmel_CG8073  Pgm2a; phosphoglucomutase 2a [KO:K01835] [EC:5.4.2.2]\n            Dmel_CG8094  Hex-C; hexokinase C [KO:K00844] [EC:2.7.1.1]\n            Dmel_CG8251  Pgi; phosphoglucose isomerase, isoform A [KO:K01810] [EC:5.3.1.9]\n            Dmel_CG8893  Gapdh2; glyceraldehyde 3 phosphate dehydrogenase 2, isoform C [KO:K00134] [EC:1.2.1.12]\n            Dmel_CG9008  CG9008; uncharacterized protein, isoform D [KO:K01792] [EC:5.1.3.15]\n            Dmel_CG9010  CG9010; uncharacterized protein [KO:K00134] [EC:1.2.1.12]\n            Dmel_CG9390  AcCoAS; acetyl coenzyme A synthase, isoform D [KO:K01895] [EC:6.2.1.1]\n            Dmel_CG9629  Aldh7A1; aldehyde dehydrogenase 7 family member A1 [KO:K14085] [EC:1.2.1.31 1.2.1.8 1.2.1.3]\n            Dmel_CG9961  CG9961; uncharacterized protein, isoform B [KO:K00927] [EC:2.7.2.3]\nCOMPOUND    C00022  Pyruvate\n            C00024  Acetyl-CoA\n            C00031  D-Glucose\n            C00033  Acetate\n            C00036  Oxaloacetate\n            C00068  Thiamin diphosphate\n            C00074  Phosphoenolpyruvate\n            C00084  Acetaldehyde\n            C00085  D-Fructose 6-phosphate\n            C00103  D-Glucose 1-phosphate\n            C00111  Glycerone phosphate\n            C00118  D-Glyceraldehyde 3-phosphate\n            C00186  (S)-Lactate\n            C00197  3-Phospho-D-glycerate\n            C00221  beta-D-Glucose\n            C00236  3-Phospho-D-glyceroyl phosphate\n            C00267  alpha-D-Glucose\n            C00354  D-Fructose 1,6-bisphosphate\n            C00469  Ethanol\n            C00631  2-Phospho-D-glycerate\n            C00668  alpha-D-Glucose 6-phosphate\n            C01159  2,3-Bisphospho-D-glycerate\n            C01172  beta-D-Glucose 6-phosphate\n            C01451  Salicin\n            C05125  2-(alpha-Hydroxyethyl)thiamine diphosphate\n            C06186  Arbutin\n            C06187  Arbutin 6-phosphate\n            C06188  Salicin 6-phosphate\n            C15972  Enzyme N6-(lipoyl)lysine\n            C15973  Enzyme N6-(dihydrolipoyl)lysine\n            C16255  [Dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine\nREFERENCE   \n  AUTHORS   Nishizuka Y (ed).\n  TITLE     [Metabolic Maps] (In Japanese)\n  JOURNAL   Tokyo Kagaku Dojin (1980)\nREFERENCE   \n  AUTHORS   Nishizuka Y, Seyama Y, Ikai A, Ishimura Y, Kawaguchi A (eds).\n  TITLE     [Cellular Functions and Metabolic Maps] (In Japanese)\n  JOURNAL   Tokyo Kagaku Dojin (1997)\nREFERENCE   \n  AUTHORS   Michal G.\n  TITLE     Biochemical Pathways\n  JOURNAL   Wiley (1999)\nREL_PATHWAY dme00020  Citrate cycle (TCA cycle)\n            dme00030  Pentose phosphate pathway\n            dme00500  Starch and sucrose metabolism\n            dme00620  Pyruvate metabolism\n            dme00640  Propanoate metabolism\nKO_PATHWAY  ko00010\n///")
 8.             └─ffrec$setBody(value)

[ FAIL 1 | WARN 6 | SKIP 0 | PASS 562 ]
Error: Test failures
Execution halted